781 tool(s) found

Tool Description Topics Available version(s)
Add column to an existing dataset 3
Add expression data (RNAseq or Immuno-assays)[Human Protein Atlas] 2
Add protein features [neXtProt] 2
Add protein features (Mouse) [UniProt] 1
AddCommentsToBam add comments to BAM dataset 11
AddOrReplaceReadGroups add or replaces read group information 11
Aggregate datapoints Appends the average, min, max of datapoints per interval 1
Align reads and estimate abundance on a de novo assembly of RNA-Seq data 11
Align sequences using a variety of alignment methods (align_seqs) 3
Align.check Calculate the number of potentially misaligned bases 5
Align.seqs Align sequences to a template alignment 5
Amova Analysis of molecular variance 5
Analyze statistical significance of sample groupings using distance matrices (compare_categories) 3
Annotate a VCF dataset with custom filters 2
AnnotateBed annotate coverage of features from multiple files 17
Anosim Non-parametric multivariate analysis of changes in community structure 5
Anova N-way anova. With ou Without interactions 5
antigenic Predicts potentially antigenic regions of a protein sequence, using the method of Kolaskar and Tongaonkar. 4
ASCA Splitting of the total variance into independent blocks according to the experimental factors and multivariate analysis (SCA) of each block 1
Assign taxonomy to each sequence (assign_taxonomy) 3
backtranseq Back translate a protein sequence 5
BAM filter Removes reads from a BAM file based on criteria 5
BAM to BED converter 21
BAM to Wiggle converts all types of RNA-seq data from .bam to .wig 9
BAM-to-SAM convert BAM to SAM 8
BAM/SAM Mapping Stats reads mapping statistics for a provided BAM or SAM file. 9
bamCompare normalizes and compares two BAM files to obtain the ratio, log2ratio or difference between them 16
bamCoverage generates a coverage bigWig file from a given BAM file 16
BamLeftAlign indels in BAM datasets 7
bamPEFragmentSize Estimate the predominant cDNA fragment length from paired-end sequenced BAM/CRAM files 16
banana Bending and curvature plot in B-DNA 5
bank_inhouse search by accurate mass (and by Retention time) on a local bank 2
Barcode Splitter 6
Batch_correction Corrects intensities for signal drift and batch-effects 8
bcftools call SNP/indel variant calling from VCF/BCF 7
bcftools cnv Call copy number variation from VCF B-allele frequency (BAF) and Log R Ratio intensity (LRR) values 3
bcftools consensus Create consensus sequence by applying VCF variants to a reference fasta file 3
bcftools csq Haplotype aware consequence predictor 3
bcftools norm Left-align and normalize indels; check if REF alleles match the reference; split multiallelic sites into multiple rows; recover multiallelics from multiple rows 3
BED to BAM converter 18
BED to IGV create batch script for taking IGV screenshots 10
BED-to-bigBed converter Conversion 2
BED-to-GFF converter Conversion 1
BED12 to BED6 converter 17
BedCov calculate read depth for a set of genomic intervals 4
BEDPE to BAM converter 18
BedToIntervalList convert coordinate data into picard interval list format 11
Between-table Correlation Correlation table between two tables and graphic representation 1
bigwigCompare normalizes and compares two bigWig files to obtain the ratio, log2ratio or difference between them 16
Bin.seqs Order Sequences by OTU 5
biosed Replace or delete sequence sections 5
Biosigner Molecular signature discovery from omics data 3
BLAST XML to tabular Convert BLAST XML output to tabular Conversion 16
Bowtie2 - map reads against reference genome 22
btwisted Calculates the twisting in a B-DNA sequence 5
Build a UPGMA tree comparing samples (upgma_cluster) 2
Build expression matrix for a de novo assembly of RNA-Seq data by Trinity 11
Build Protein-Protein interaction network [BioGRID, BioPlex, HuMAP] 1
Build tissue-specific expression dataset [Human Protein Atlas](no input required) 2
cai CAI codon adaptation index 5
cai custom CAI codon adaptation index using custom codon usage file 5
Calculate alpha diversity on each sample in an otu table, using a variety of alpha diversity metrics (alpha_diversity) 3
Calculate beta diversity (pairwise sample dissimilarity) on one or many otu tables (beta_diversity) 3
CalMD recalculate MD/NM tags 3
CAMERA.annotate CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition. 8
CAMERA.combinexsAnnos Wrapper function for the combinexsAnnos CAMERA function. Returns a dataframe with recalculated annotations. 8
Change Case of selected columns 1
chaos Create a chaos game representation plot for a sequence 5
charge Protein charge plot 4
Check Format Checking/formatting the sample and variable names of the dataMatrix, sampleMetadata, and variableMetadata files 4
Check user's metadata mapping file for required data, valid format (validate_mapping_file) 2
checktrans Reports STOP codons and ORF statistics of a protein 4
Chimera.bellerophon Find putative chimeras using bellerophon 5
Chimera.ccode Find putative chimeras using ccode 5
Chimera.check Find putative chimeras using chimeraCheck 5
Chimera.perseus Find putative chimeras using chimeraCheck 5
Chimera.pintail Find putative chimeras using pintail 5
Chimera.slayer Find putative chimeras using slayer 5
Chimera.uchime Find putative chimeras using uchime 5
Chimera.vsearch find potential chimeric sequences using vsearch 3
chips Codon usage statistics 5
Chop.seqs Trim sequences to a specified length 5
Circos visualizes data in a circular layout 3
Circos: Alignments to links reformats alignment files to prepare for Circos 1
Circos: bigWig to Scatter reformats bigWig files to prepare for Circos 2d scatter/line/histogram plots 1
Circos: Bundle Links reduce numbers of links in datasets before plotting 1
Circos: Interval to Circos Text Labels reformats interval files to prepare for Circos text labels 1
Circos: Interval to Tiles reformats interval files to prepare for Circos tile plots 1
Circos: Link Density Track reduce links to a density plot 1
Circos: Resample 1/2D data reduce numbers of points in a dataset before plotting 1
Circos: Table viewer easily creates circos plots from tabular data 1
cirdna Draws circular maps of DNA constructs 5
Classify.otu Assign sequences to taxonomy 5
Classify.rf description 2
Classify.seqs Assign sequences to taxonomy 5
Classify.tree Get a consensus taxonomy for each node on a tree 5
CleanSam perform SAM/BAM grooming 11
Clearcut Generate a tree using relaxed neighbor joining 5
Clip adapter sequences 5
Clipping Profile estimates clipping profile of RNA-seq reads from BAM or SAM file 9
Closed-reference OTU picking Shotgun UniFrac workflow (pick_closed_reference_otus) 3
ClosestBed find the closest, potentially non-overlapping interval 17
ClustalW multiple sequence alignment program for DNA or proteins 4
Cluster Assign sequences to OTUs (Operational Taxonomic Unit) 5
Cluster.classic Assign sequences to OTUs (Dotur implementation) 5
Cluster.fragments Group sequences that are part of a larger sequence 5
Cluster.split Assign sequences to OTUs and split large matrices 4
ClusterBed cluster overlapping/nearby intervals 17
CML to InChI 2
CML to mol2 2
CML to SDF 2
codcmp Codon usage table comparison 5
coderet Extract CDS, mRNA and translations from feature tables 5
Collapse sequences 4
Collapse Collection into single dataset in order of the collection 4
Collapse samples Collapse samples in a BIOM table and mapping file 1
Collect Alignment Summary Metrics writes a file containing summary alignment metrics 11
Collect.shared Generate collector's curves for calculators on OTUs 5
Collect.single Generate collector's curves for OTUs 6
CollectBaseDistributionByCycle charts the nucleotide distribution per cycle in a SAM or BAM dataset 11
CollectGcBiasMetrics charts the GC bias metrics 11
CollectHsMetrics compute metrics about datasets generated through hybrid-selection (e.g. exome) 1
CollectInsertSizeMetrics plots distribution of insert sizes 11
CollectRnaSeqMetrics collect metrics about the alignment of RNA to various functional classes of loci in the genome 12
CollectWgsMetrics compute metrics for evaluating of whole genome sequencing experiments 11
Combine FASTA and QUAL into FASTQ 3
Compare two Datasets to find common or distinct rows 1
ComplementBed Extract intervals not represented by an interval file 18
compseq Count composition of dimer/trimer/etc words in a sequence 4
Compute beta diversity distance matrices and generate PCoA plots (beta_diversity_through_plots) 2
Compute both the depth and breadth of coverage of features in file B on the features in file A (bedtools coverage) 18
Compute contig Ex90N50 statistic and Ex90 transcript count from a Trinity assembly 10
Compute quality statistics 4
Compute sequence length 5
computeGCBias Determine the GC bias of your sequenced reads 16
computeMatrix prepares data for plotting a heatmap or a profile of given regions 16
Concatenate FASTA alignment by species 2
Concatenate datasets tail-to-head 1
Consensus.seqs Find a consensus sequence for each OTU or phylotype 5
Convert delimiters to TAB 1
Convert BCF to uncompressed BCF 1
Convert BED to Feature Location Index 1
Convert BED to GFF 1
Convert Biom1 to Biom2 1
Convert Biom2 to Biom1 1
Convert CSV to tabular 1
Convert FASTA to 2bit 2
Convert FASTA to Bowtie base space Index 1
Convert FASTA to Bowtie color space Index 1
Convert FASTA to fai file 1
Convert FASTA to len file 1
Convert FASTA to Tabular 1
Convert Genomic Intervals To BED 1
Convert Genomic Intervals To Coverage 2
Convert Genomic Intervals To Strict BED 1
Convert Genomic Intervals To Strict BED12 1
Convert Genomic Intervals To Strict BED6 1
Convert GFF to BED 1
Convert GFF to Feature Location Index 1
Convert Len file to Linecount 1
Convert lped to fped 1
Convert lped to plink pbed 1
Convert MAF to Fasta 1
Convert MAF to Genomic Intervals 1
Convert Picard Interval List to BED6 converter 1
Convert plink pbed to ld reduced format 1
Convert plink pbed to linkage lped 1
Convert Ref taxonomy to Seq Taxonomy converts 2 or 3 column sequence taxonomy file to a 2 column mothur taxonomy_outline format 1
Convert SAM to interval 2
Convert SAM to BAM without sorting 1
Convert tabular to CSV 1
Convert tabular to dbnsfp 1
Convert tar to directory 1
Convert uncompressed BCF to BCF 1
Cooccurrence tests whether presence-absence patterns differ from chance 5
Corr.axes correlation of data to axes 5
correctGCBias uses the output from computeGCBias to generate GC-corrected BAM/CRAM files 16
Correlation for numeric columns 2
Count occurrences of each record 2
Count GFF Features 3
Count the sequences in a fasta file (count_seqs) 2
Count.groups counts the number of sequences represented by a specific group or set of groups 5
Count.seqs (aka make.table) counts the number of sequences represented by the representative 5
cpgplot Plot CpG rich areas 5
cpgreport Reports all CpG rich regions 4
Create assemblies with Unicycler 7
Create single interval as a new dataset 1
Create three-dimensional PCoA plots to be visualized with Emperor (make_emperor) 2
Create.database creates a database file from a list, repnames, repfasta and contaxonomy file 4
Cuffcompare compare assembled transcripts to a reference annotation and track Cufflinks transcripts across multiple experiments 14
Cufflinks transcript assembly and FPKM (RPKM) estimates for RNA-Seq data 11
Cuffmerge merge together several Cufflinks assemblies 12
cusp Create a codon usage table 5
Cut columns from a table 2
Cutadapt Remove adapter sequences from Fastq/Fasta 13
cutseq Removes a specified section from a sequence 4
dan Calculates DNA RNA/DNA melting temperature 4
Data Fetch 1
DAVID functional annotation for a list of genes 1
Degap.seqs Remove gap characters from sequences 5
degapseq Removes gap characters from sequences 5
Deletion Profile calculates the distributions of deleted nucleotides across reads 3
Describe samples and replicates 9
descseq Alter the name or description of a sequence 5
DESeq2 Determines differentially expressed features from count tables Differential gene expression analysis 15
Determine_batch_correction to choose between linear, lowess and loess methods 5
Deunique.seqs Return all sequences 5
Deunique.tree Reinsert the redundant sequence identiers back into a unique tree. 5
DEXSeq Determines differential exon usage from count tables 5
DEXSeq-Count Prepare and count exon abundancies from RNA-seq data 5
DiffBind differential binding analysis of ChIP-Seq peak data 12
Differential expression analysis using a Trinity assembly 11
diffseq Find differences between nearly identical sequences 4
digest Protein proteolytic enzyme or reagent cleavage digest 5
Dist.seqs calculate uncorrected pairwise distances between aligned sequences 5
Dist.shared Generate a phylip-formatted dissimilarity distance matrix among multiple groups 5
dotmatcher Displays a thresholded dotplot of two sequences 4
dotpath Non-overlapping wordmatch dotplot of two sequences 4
dottup Displays a wordmatch dotplot of two sequences 4
Download and Extract Reads in BAM format from NCBI SRA 12
Download and Extract Reads in FASTA/Q format from NCBI SRA 12
Download and Generate Pileup Format from NCBI SRA 11
Downsample SAM/BAM Downsample a file to retain a subset of the reads 11
Draw nucleotides distribution chart 4
Draw quality score boxplot 5
Draw ROC plot on "Perform LDA" output 3
dreg Regular expression search of a nucleotide sequence 5
edgeR Perform differential expression of count data 4
einverted Finds DNA inverted repeats 4
Enrichment analysis for Gene Ontology (Human, Mouse, Rat)[topGO] 3
epestfind Finds PEST motifs as potential proteolytic cleavage sites 4
equicktandem Finds tandem repeats 4
est2genome Align EST and genomic DNA sequences 4
EstimateLibraryComplexity assess sequence library complexity from read sequences 11
etandem Looks for tandem repeats in a nucleotide sequence 4
ExpandBed replicate lines based on lists of values in columns 17
Extract and cluster differentially expressed transcripts from a Trinity assembly 10
Extract features from GFF data 1
Extract MAF by block number given a set of block numbers and a MAF file 1
Extract Pairwise MAF blocks given a set of genomic intervals 1
extractfeat Extract features from a sequence 4
extractseq Extract regions from a sequence 5
FASTA Width formatter 4
FASTA-to-Tabular converter 3
Faster Download and Extract Reads in FASTQ format from NCBI SRA 1
FASTQ de-interlacer on paired end reads 3
FASTQ Groomer convert between various FASTQ quality formats 4
FASTQ interlacer on paired end reads 4
FASTQ joiner on paired end reads 6
FASTQ Masker by quality score 3
FASTQ Quality Trimmer by sliding window 5
FASTQ splitter on joined paired end reads 3
FASTQ Summary Statistics by column Sequence assembly validation 3
FASTQ to FASTA converter from FASTX-toolkit Sequence conversion 5
FASTQ to Tabular converter 4
FASTQ Trimmer by column 4
Fastq.info Convert fastq to fasta and quality 5
FastQC Read Quality reports Sequence composition calculation Sequencing quality control Statistical calculation 17
FastqToSam convert Fastq data into unaligned BAM 14
featureCounts Measure gene expression in RNA-Seq experiments from SAM or BAM files. Sequence assembly 16
Filter data on any column using simple expressions Formatting 1
Filter by keywords and/or numerical value 2
Filter by quality 5
Filter Combined Transcripts using tracking file 1
Filter fasta to remove sequences based on input criteria (filter_fasta) 2
Filter FASTQ reads by quality score and length 4
Filter GFF data by attribute using simple expressions 3
Filter GFF data by feature count using simple expressions 2
Filter GTF data by attribute values_list 1
Filter low expression transcripts from a Trinity assembly 11
Filter MAF by specified attributes 1
Filter MAF blocks by Size 1
Filter MAF blocks by Species 1
Filter OTUs from an OTU table based on their observation counts or identifier (filter_otus_from_otu_table) 2
Filter pileup on coverage and SNPs 3
Filter SAM on bitwise flag values 2
Filter SAM or BAM, output SAM or BAM files on FLAG MAPQ RG LN or by region 6
Filter sequence alignment by removing highly variable regions (filter_alignment) 3
Filter sequences by length Filtering 5
Filter taxa from an OTU table (filter_taxa_from_otu_table) 2
Filter.seqs removes columns from alignments 5
Filter.shared remove OTUs based on various critieria 5
Filters samples from an OTU table on the basis of the number of observations in that sample, or on the basis of sample metadata (filter_samples_from_otu_table) 2
FilterSamReads include or exclude aligned and unaligned reads and read lists 11
FisherBed calculate Fisher statistic between two feature files 17
FixMateInformation ensure that all mate-pair information is in sync between each read and it's mate pair 11
Flagstat tabulate descriptive stats for BAM datset 8
FlankBed create new intervals from the flanks of existing intervals 18
Format Fastq sequences and barcode data (extract_barcodes) 2
FPKM Count calculates raw read count, FPM, and FPKM for each gene 5
freak Residue/base frequency table or plot 4
FreeBayes bayesian genetic variant detector 7
fuzznuc Nucleic acid pattern search 5
fuzzpro Protein pattern search 4
fuzztran Protein pattern search after translation 4
g:Profiler tools for functional profiling of gene lists 1
garnier Predicts protein secondary structure 5
GC Skew calculates skew over genomic sequences 1
geecee Calculates fractional GC content of nucleic acid sequences 5
Gene BED To Exon/Intron/Codon BED expander 1
Gene Body Coverage (BAM) Read coverage over gene body. 11
Gene Body Coverage (Bigwig) Read coverage over gene body 11
Generate A Matrix for using PC and LDA 2
Generate gene to transcript map for Trinity assembly 11
Generate pileup from BAM dataset 3
Generate SuperTranscripts from a Trinity assembly 5
Generic_Filter Removes elements according to numerical or qualitative values 4
Genome Coverage compute the coverage over an entire genome 18
Get expression profiles by (normal or tumor) tissue/cell type [Human Protein Atlas] 2
Get MS/MS observations in tissue/fluid [Peptide Atlas] 2
Get.communitytype description 5
Get.coremicrobiome fraction of OTUs for samples or abundances 5
Get.dists selects distances from a phylip or column file 5
Get.group group names from shared or from list and group 5
Get.groups Select groups 5
Get.label label names from list, sabund, or rabund file 5
Get.lineage Picks by taxon 5
Get.mimarkspackage creates a mimarks package form with your groups 5
Get.otulabels Selects OTU labels 5
Get.otulist Get otus for each distance in a otu list 5
Get.oturep Generate a fasta with a representative sequence for each OTU 5
Get.otus Get otus containing sequences from specified groups 5
Get.rabund Get rabund from a otu list or sabund 5
Get.relabund Calculate the relative abundance of each otu 5
Get.sabund Get sabund from a otu list or rabund 5
Get.seqs Picks sequences by name 5
Get.sharedseqs Get shared sequences at each distance from list and group 5
GetFastaBed use intervals to extract sequences from a FASTA file 17
getorf Finds and extracts open reading frames (ORFs) 4
GFF-to-BED converter Conversion 1
GffCompare compare assembled transcripts to a reference annotation 2
GMAJ Multiple Alignment Viewer 1
GO terms classification and enrichment analysis (Human, Mouse, Rat)[clusterProfiler] 3
Golm Metabolome Database search spectrum : GC-MS Mass Spectral Database. 2
Group data by a column and perform aggregate operation on other columns. 3
GroupByBed group by common cols and summarize other cols 17
Hcluster Assign sequences to OTUs (Operational Taxonomic Unit) 2
Heatmap Heatmap of the dataMatrix 3
HeatMap (Cluster and visualize the results) 1
Heatmap.bin Generate a heatmap for OTUs 5
Heatmap.sim Generate a heatmap for pariwise similarity 5
heatmap2 4
helixturnhelix Report nucleic acid binding motifs 4
Hexamer frequency calculates hexamer (6mer) frequency for reads, genomes, and mRNA sequences 3
HISAT2 A fast and sensitive alignment program 16
Histogram of a numeric column 4
HMDB MS search search by masses on HMDB online LCMS bank 3
hmoment Hydrophobic moment calculation 4
Homova Homogeneity of molecular variance 5
htseq-count - Count aligned reads in a BAM file that overlap features in a GFF file 9
ID choice Choosing a particular column in your metadata to be considered as Identifiers 1
ID Converter (Human, Mouse, Rat) 3
IdxStats tabulate mapping statistics for BAM dataset 9
iep Calculates the isoelectric point of a protein 4
InChI to CML 2
InChI to MOL 2
InChI to MOL2 2
InChI to SDF 2
Indicator Identify indicator "species" for nodes on a tree 5
Infer Experiment speculates how RNA-seq were configured 11
infoseq Displays some simple information about sequences 5
Inner Distance calculate the inner distance (or insert size) between two paired RNA reads 11
Insertion Profile calculates the distribution of inserted nucleotides across reads 3
Intensity Check Statistical measures, number of missing values and mean fold change 1
Intersect intervals find overlapping intervals in various ways 17
isochore Plots isochores in large DNA sequences 4
JaccardBed calculate the distribution of relative distances between two files 17
Join MAF blocks by Species 1
Join two Datasets side by side on a specified field 3
Junction Annotation compares detected splice junctions to reference gene model 11
Junction Saturation detects splice junctions from each subset and compares them to reference gene model 11
Kallisto pseudo - run pseudoalignment on RNA-Seq transcripts 2
Kallisto quant - quantify abundances of RNA-Seq transcripts 4
Kraken assign taxonomic labels to sequencing reads 6
Kraken-filter filter classification by confidence score 3
Kraken-mpa-report view report of classification for multiple samples 5
Kraken-report view sample report of a classification 4
Kraken-translate convert taxonomy IDs to names 3
LASTZ : align long sequences 5
LASTZ_D : estimate substitution scores matrix 3
LCMS matching Annotation of LCMS peaks using matching on a in-house spectra database or on PeakForest spectra database. 8
LD linkage disequilibrium and tag SNPs 1
Lefse description 5
Libshuff Cramer-von Mises tests communities for the same structure 5
limma Perform differential expression with limma-voom or limma-trend 10
lindna Draws linear maps of DNA constructs 4
Line/Word/Character count of a dataset 1
LinksBed create a HTML page of links to UCSC locations 17
Lipidmaps : search on LIPID MAPS Structure Database (LMSD) online with masses and its Text/Ontology-based search engine. 2
List.otulabels Lists otu labels from shared or relabund file 5
List.seqs Lists the names (accnos) of the sequences 5
MACS2 bdgbroadcall Call broad peaks from bedGraph output Regulatory element prediction 8
MACS2 bdgcmp Deduct noise by comparing two signal tracks in bedGraph Regulatory element prediction 8
MACS2 bdgdiff Differential peak detection based on paired four bedgraph files Regulatory element prediction 9
MACS2 bdgpeakcall Call peaks from bedGraph output Regulatory element prediction 8
MACS2 callpeak Call peaks from alignment results Regulatory element prediction 11
MACS2 filterdup Remove duplicate reads at the same position Regulatory element prediction 8
MACS2 predictd Predict 'd' or fragment size from alignment results Regulatory element prediction 8
MACS2 randsample Randomly sample number or percentage of total reads Regulatory element prediction 8
MACS2 refinepeak Refine peak summits and give scores measuring balance of forward- backward tags (Experimental) Regulatory element prediction 8
MAF Coverage Stats Alignment coverage information 1
MAF to BED Converts a MAF formatted file to the BED format 1
MAF to FASTA Converts a MAF formatted file to FASTA format 1
MAF to Interval Converts a MAF formatted file to the Interval format 1
MAFFT Multiple alignment program for amino acid or nucleotide sequences 4
Make Design Assign groups to Sets 5
Make OTU table Make an OTU table from an OTU map and a taxonomy assignment file 1
Make phylogeny (make_phylogeny) 2
Make taxonomy summary charts based on taxonomy assignment (plot_taxa_summary) 2
Make.biom Make biom files from a shared file 5
Make.contigs Aligns paired forward and reverse fastq files to contigs as fasta and quality 5
Make.fastq Convert fasta and quality to fastq 5
Make.group Make a group file 6
Make.lefse create a lefse formatted input file from mothur's output files 5
Make.lookup allows you to create custom lookup files for use with shhh.flows 5
Make.shared Make a shared file from a list and a group 6
Make.sra creates the necessary files for a NCBI submission 5
MakeWindowsBed make interval windows across a genome 18
Manipulate FASTQ reads on various attributes 3
Mantel Mantel correlation coefficient between two matrices. 5
Map with BWA - map short reads (< 100 bp) against reference genome 15
Map with BWA-MEM - map medium and long reads (> 100 bp) against reference genome DNA mapping Genetic mapping Genome annotation Mapping Mapping assembly Protein SNP mapping Sequence assembly Sequence tag mapping 17
MapBed apply a function to a column for each overlapping interval 17
MarkDuplicates examine aligned records in BAM datasets to locate duplicate molecules 11
MarkDuplicatesWithMateCigar examine aligned records in BAM datasets to locate duplicate molecules 11
marscan Finds MAR/SAR sites in nucleic sequences 5
MaskFastaBed use intervals to mask sequences from a FASTA file 17
maskfeat Mask off features of a sequence 5
maskseq Mask off regions of a sequence 5
MassBank spectrum searches : Search by pseudo-spectra on a High Quality Mass Spectral Database. 1
MasterVar to pgSnp Convert from MasterVar to pgSnp format 1
matcher Finds the best local alignments between two sequences 4
MeanQualityByCycle chart distribution of base qualities 11
megamerger Merge two large overlapping nucleic acid sequences 4
Merge BAM Files merges BAM files together 3
Merge BedGraph files combines coverage intervals from multiple BEDGRAPH files 17
Merge Columns together 2
Merge.files Merge data 5
Merge.groups Merge groups in a shared file 5
Merge.sfffiles Merge SFF files 5
Merge.taxsummary Merge tax.summary files 5
MergeBamAlignment merge alignment data with additional info stored in an unmapped BAM dataset 11
MergeBED combine overlapping/nearby intervals into a single interval 17
merger Merge two overlapping nucleic acid sequences 4
MergeSamFiles merges multiple SAM/BAM datasets into one 11
metaMS.runGC GC-MS data preprocessing using metaMS package 4
Metastats generate principle components plot data 5
Mimarks.attributes Reads bioSample Attributes xml and generates source for get.mimarkspackage command 5
Mismatch Profile calculates the distribution of mismatches across reads 3
mixmodel ANOVA for repeated measures statistics 1
MOL to CML 2
MOL to MOL2 2
MOL2 to CML 2
MOL2 to InChI 2
MOL2 to MOL 2
MOL2 to SDF 2
MPileup call variants 10
msbar Mutate sequence beyond all recognition 4
MSnbase readMSData Imports mass-spectrometry data files 2
multiBamSummary calculates average read coverages for a list of two or more BAM/CRAM files 17
multiBigwigSummary calculates average scores for a list of two or more bigwig files 17
MultiCovBed counts coverage from multiple BAMs at specific intervals 17
Multilevel Data transformation: Within matrix decomposition for repeated measurements (cross-over design) with mixOmics package 1
Multiple Intersect identifies common intervals among multiple interval files 21
MultiQC aggregate results from bioinformatics analyses into a single report Statistical calculation Validation Visualisation 9
Multivariate PCA, PLS and OPLS 7
NCBI BLAST+ blastdbcmd entry(s) Extract sequence(s) from BLAST database Data retrieval Database search 16
NCBI BLAST+ blastn Search nucleotide database with nucleotide query sequence(s) Data retrieval Database search Sequence similarity search 17
NCBI BLAST+ blastp Search protein database with protein query sequence(s) Data retrieval Database search Sequence similarity search 17
NCBI BLAST+ blastx Search protein database with translated nucleotide query sequence(s) Data retrieval Database search Sequence similarity search 16
NCBI BLAST+ convert2blastmask Convert masking information in lower-case masked FASTA input to file formats suitable for makeblastdb Conversion 12
NCBI BLAST+ database info Show BLAST database information from blastdbcmd Data retrieval 16
NCBI BLAST+ dustmasker masks low complexity regions Sequence complexity calculation 14
NCBI BLAST+ makeblastdb Make BLAST database Genome indexing 17
NCBI BLAST+ makeprofiledb Make profile database Genome indexing 10
NCBI BLAST+ rpsblast Search protein domain database (PSSMs) with protein query sequence(s) Data retrieval Database search Sequence similarity search 15
NCBI BLAST+ rpstblastn Search protein domain database (PSSMs) with translated nucleotide query sequence(s) Data retrieval Database search Sequence similarity search 15
NCBI BLAST+ segmasker low-complexity regions in protein sequences Sequence complexity calculation 12
NCBI BLAST+ tblastn Search translated nucleotide database with protein query sequence(s) Data retrieval Database search Sequence similarity search 17
NCBI BLAST+ tblastx Search translated nucleotide database with translated nucleotide query sequence(s) Data retrieval Database search Sequence similarity search 17
needle Needleman-Wunsch global alignment 4
newcpgreport Report CpG rich areas 4
newcpgseek Reports CpG rich region 4
newseq Type in a short new sequence 5
Nmds generate non-metric multidimensional scaling data 5
NMR spectra alignment based on the Cluster-based Peak Alignment (CluPA) algorithm 3
NMR_Annotation Annotation of complex mixture NMR spectra and metabolite proportion estimation 1
NMR_Bucketing Bucketing and integration of NMR Bruker raw data 5
NMR_Preprocessing Preprocessing of 1D NMR spectra 3
NMR_Read Read Bruker NMR raw files 2
noreturn Removes carriage return from ASCII files 5
Normalization Normalization of (preprocessed) spectra 4
Normalize.shared Normalize the number of sequences per group to a specified level 5
NormalizeFasta normalize fasta datasets 11
notseq Exclude a set of sequences and write out the remaining ones 5
nthseq Writes one sequence from a multiple set of sequences 4
NucBed profile the nucleotide content of intervals in a FASTA file 17
octanol Displays protein hydropathy 4
oddcomp Find protein sequence regions with a biased composition 4
Otu.association Calculate the correlation coefficient for the otus 5
Otu.hierarchy Relate OTUs at different distances 5
OverlapBed computes the amount of overlap from two intervals 17
Pairwise.seqs calculate uncorrected pairwise distances between sequences 5
palindrome Looks for inverted repeats in a nucleotide sequence 4
Parse.list Generate a List file for each group 5
Parsimony Describes whether two or more communities have the same structure 5
Partition genes into expression clusters after differential expression analysis using a Trinity assembly 10
Paste two files side by side 1
pasteseq Insert one sequence into another 4
Pathways identification and coverage [KEGG] 1
Pathways visualization of (differentially expressed) genes/proteins [KEGG] 1
patmatdb Search a protein sequence with a motif 5
Pca Principal Coordinate Analysis for a shared file 5
Pcoa Principal Coordinate Analysis for a distance matrix 4
Pcr.seqs Trim sequences 5
pepcoil Predicts coiled coil regions 4
pepinfo Plots simple amino acid properties in parallel 4
pepnet Displays proteins as a helical net 5
pepstats Protein statistics 5
pepwheel Shows protein sequences as helices 4
pepwindow Displays protein hydropathy 4
pepwindowall Displays protein hydropathy of a set of sequences 4
Perform alpha rarefaction (alpha_rarefaction) 3
Perform jackknifed UPGMA clustering and building jackknifed PCoA plots (jackknifed_beta_diversity) 2
Perform open-reference OTU picking (pick_open_reference_otus) 3
Perform OTU picking (pick_otus) 2
Perform taxonomy summaries and plots (summarize_taxa_through_plots) 2
Phylo.diversity Alpha Diversity calculates unique branch length 5
Phylotype Assign sequences to OTUs based on taxonomy 5
Picard Collect Sequencing Artifact Metrics Collect metrics to quantify single-base sequencing artifacts 1
Pick representative set of sequences (pick_rep_set) 2
Pileup-to-Interval condenses pileup format into ranges of bases 5
Plot heatmap of OTU table (make_otu_heatmap) 2
plotcon Plot quality of conservation of a sequence alignment 4
plotCorrelation Create a heatmap or scatterplot of correlation scores between different samples 16
plotCoverage assesses the sequencing depth of BAM/CRAM files 16
plotDEXSeq Visualization of the per gene DEXSeq results 1
plotEnrichment plots read/fragment coverage over sets of regions 12
plotFingerprint plots profiles of BAM files; useful for assessing ChIP signal strength 16
plotHeatmap creates a heatmap for score distributions across genomic regions 17
plotorf Plot potential open reading frames 5
plotPCA Generate principal component analysis (PCA) plots from multiBamSummary or multiBigwigSummary output 16
plotProfile creates a profile plot for score distributions across genomic regions 16
Plotting tool for multiple series and graph types 4
polydot Displays all-against-all dotplots of a set of sequences 4
Pre.cluster Remove sequences due to pyrosequencing errors 5
preg Regular expression search of a protein sequence 5
prettyplot Displays aligned sequences, with colouring and boxing 4
prettyseq Output sequence with translated ranges 4
Primer.design identify sequence fragments that are specific to particular OTUs 5
primersearch Searches DNA sequences for matches with primer pairs 4
proFIA Preprocessing of FIA-HRMS data 4
Prokka Prokaryotic genome annotation 5
Quality format converter (ASCII-Numeric) 4
Quality Metrics Metrics and graphics to check the quality of the data 5
QualityScoreDistribution chart quality score distribution 11
Quast Genome assembly Quality 5
Query pathway database [Reactome] 2
RandomBed generate random intervals in a genome 18
Rarefaction.shared Generate inter-sample rarefaction curves for OTUs 5
Rarefaction.single Generate intra-sample rarefaction curves for OTUs 5
Read Distribution calculates how mapped reads were distributed over genome feature 11
Read Duplication determines reads duplication rate with sequence-based and mapping-based strategies 9
Read GC determines GC% and read count 9
Read NVC to check the nucleotide composition bias 9
Read Quality determines Phred quality score 9
Reheader copy SAM/BAM header between datasets 2
ReldistBed calculate the distribution of relative distances 17
Remove beginning of a file 1
Remove sequencing artifacts 5
Remove.dists Removes distances from a phylip or column file 5
Remove.groups Remove groups from groups,fasta,names,list,taxonomy 5
Remove.lineage Picks by taxon 5
Remove.otulabels Removes OTU labels 4
Remove.otus Removes OTUs from various file formats 5
Remove.rare Remove rare OTUs 5
Remove.seqs Remove sequences by name 5
Rename sequences 5
ReorderSam reorder reads to match ordering in reference sequences 14
ReplaceSamHeader replace header in a SAM/BAM dataset 14
Reverse Complement a MAF file 1
Reverse-Complement 5
Reverse.seqs Reverse complement the sequences 5
RevertOriginalBaseQualitiesAndAddMateCigar revert the original base qualities and add the mate cigar tag 11
RevertSam revert SAM/BAM datasets to a previous state 11
revseq Reverse and complement a sequence 5
RmDup remove PCR duplicates 8
RNA fragment size calculates the fragment size for each gene/transcript 5
RNA STAR Gapped-read mapper for RNA-seq data Mapping assembly 11
RNA/DNA converter 5
RNASeq samples quality check for transcript quantification 11
RPKM Saturation calculates raw count and RPKM values for transcript at exon, intron, and mRNA level 11
Run a core set of QIIME diversity analyses (core_diversity_analyses) 3
Run join_paired_ends on multiple files (multiple_join_paired_ends) 2
Run split_libraries_fastq on multiple files (multiple_split_libraries_fastq) 2
Sailfish transcript quantification from RNA-seq data 4
Salmon Transcript Quantification from RNA-seq data 5
SAM-to-BAM convert SAM to BAM 11
SamToFastq extract reads and qualities from SAM/BAM dataset and convert to fastq 14
Samtools view reformat, filter, or subsample 2
Screen.seqs Screen sequences 5
SDF to CML 2
SDF to InChI 2
SDF to mol2 2
Secure Hash / Message Digest on a dataset 1
Select lines that match an expression 1
Select first lines from a dataset 1
Select last lines from a dataset 1
Select random lines from a file 2
Send to cloud 1
Sens.spec Determine the quality of OTU assignment 5
Seq.error assess error rates in sequencing data 5
seqmatchall All-against-all comparison of a set of sequences 4
seqret Reads and writes sequences 5
Sequence Logo generator for fasta (eg Clustal alignments) 3
SFF converter 1
Sffinfo Summarize the quality of sequences 5
Shhh.flows Denoise flowgrams (PyroNoise algorithm) 5
Shhh.seqs Denoise program (Quince SeqNoise) 5
showfeat Show features of a sequence 4
ShuffleBed randomly redistrubute intervals in a genome 18
shuffleseq Shuffles a set of sequences maintaining composition 4
SICER Statistical approach for the Identification of ChIP-Enriched Regions 2
Sickle windowed adaptive trimming of FASTQ data 5
sigcleave Reports protein signal cleavage sites 4
sirna Finds siRNA duplexes in mRNA 5
sixpack Display a DNA sequence with 6-frame translation and ORFs 5
skipseq Reads and writes sequences, skipping first few 4
Slice BAM by genomic regions 6
Slice VCF to get data from selected regions 2
SlopBed adjust the size of intervals 18
SnpEff Variant effect and annotation 15
SnpEff Available Databases 11
SnpEff build: database from Genbank or GFF record 6
SnpEff chromosome-info: list chromosome names/lengths 3
SnpEff Download Download a new database 15
SnpSift Annotate SNPs from dbSnp 9
SnpSift CaseControl Count samples are in 'case' and 'control' groups. 9
SnpSift Extract Fields from a VCF file inot a tabular file 6
SnpSift Filter Filter variants using arbitrary expressions 9
SnpSift Intervals Filter variants using intervals 9
SnpSift rmInfo remove INFO field annotations 7
SnpSift Variant Type Annotate with variant type 7
SnpSift vcfCheck basic checks for Vcf specification compliance 7
Sort BAM dataset 8
Sort data in ascending or descending order 2
Sort.seqs put sequences in different files in the same order 5
SortBED order the intervals 17
SortSam sort SAM/BAM dataset 11
SpacingBed reports the distances between features 13
SPAdes genome assembler for regular and single-cell projects 10
Split BAM dataset on readgroups 3
Split fastq libraries to performs demultiplexing of Fastq sequence data (split_libraries_fastq) 2
Split libraries according to barcodes specified in mapping file (split_libraries) 2
Split MAF blocks by Species 1
Split.abund Separate sequences into rare and abundant groups 5
Split.groups Generates a fasta file for each group 5
splitter Split a sequence into (overlapping) smaller sequences 4
Stacks2: clone filter Identify PCR clones 1
Stacks2: cstacks Generate catalog of loci 1
Stacks2: de novo map the Stacks pipeline without a reference genome (denovo_map.pl) 1
Stacks2: gstacks Call variants, genotypes and haplotype 1
Stacks2: kmer filter Identify PCR clones 1
Stacks2: populations Calculate population-level summary statistics 1
Stacks2: process radtags the Stacks demultiplexing script 1
Stacks2: process shortreads fast cleaning of randomly sheared genomic or transcriptomic data 1
Stacks2: reference map the Stacks pipeline with a reference genome (ref_map.pl) 1
Stacks2: sstacks Match samples to the catalog 1
Stacks2: tsv2bam Sort reads by RAD locus 1
Stacks2: ustacks Identify unique stacks 1
Stats generate statistics for BAM dataset 5
Stitch Gene blocks given a set of coding exon intervals 1
Stitch MAF blocks given a set of genomic intervals 1
StringTie transcript assembly and quantification 13
StringTie merge transcripts 7
Sub.sample Create a sub sample 5
SubtractBed remove intervals based on overlaps 17
Summarize taxa and store results in a new table or appended to an existing mapping file (summarize_taxa) 2
Summary Statistics for any numerical column 3
Summary.qual Summarize the quality scores 5
Summary.seqs Summarize the quality of sequences 5
Summary.shared Summary of calculator values for OTUs 4
Summary.single Summary of calculator values for OTUs 6
Summary.tax Assign sequences to taxonomy 5
supermatcher Match large sequences against one or more other sequences 4
syco Synonymous codon usage Gribskov statistic plot 4
T Test for Two Samples 2
Table Merge Merging dataMatrix with a metadata table 2
Tabular to FASTQ converter 4
Tabular-to-FASTA converts tabular file to FASTA format 2
TagBed tag BAM alignments based on overlaps with interval files 17
Taxonomy-to-Krona convert a mothur taxonomy file to Krona input format 3
tcode Fickett TESTCODE statistic to identify protein-coding DNA 4
textsearch Search sequence documentation. Slow, use SRS and Entrez! 5
tmap Displays membrane spanning regions 5
tranalign Align nucleic coding regions given the aligned proteins 5
Transcript Integrity Number evaluates RNA integrity at a transcript level 5
TransDecoder Find coding regions within transcripts 4
transeq Translate nucleic acid sequences 5
Transformation Transforms the dataMatrix intensity values 4
Tree.shared Generate a newick tree for dissimilarity among groups 5
Trim leading or trailing characters 1
Trim Galore! Quality and adapter trimmer of reads 8
Trim sequences 6
Trim.flows partition by barcode, trim to length, cull by length and mismatches 5
Trim.seqs Trim sequences - primers, barcodes, quality 5
trimest Trim poly-A tails off EST sequences 4
Trimmomatic flexible read trimming tool for Illumina NGS data Sequence trimming 13
trimseq Trim ambiguous bits off the ends of sequences 4
Trinity de novo assembly of RNA-Seq data 13
twofeat Finds neighbouring pairs of features in sequences 4
unifrac.unweighted Describes whether two or more communities have the same structure 5
unifrac.weighted Describes whether two or more communities have the same structure 5
union Reads sequence fragments and builds one sequence 5
Unique.seqs Return unique sequences 5
Univariate Univariate statistics 6
Upload File from your computer 2
ValidateSamFile assess validity of SAM/BAM dataset 11
VarScan for variant detection 3
VCF to MAF Custom Track for display at UCSC 1
VCF-BEDintersect: Intersect VCF and BED datasets 6
VCF-VCFintersect: Intersect two VCF datasets 7
VCFaddinfo: Adds info fields from the second dataset which are not present in the first dataset 7
VcfAllelicPrimitives: Split alleleic primitives (gaps or mismatches) into multiple VCF lines 6
VCFannotate: Intersect VCF records with BED annotations 6
VCFannotateGenotypes: Annotate genotypes in a VCF dataset using genotypes from another VCF dataset 7
VCFbreakCreateMulti: Break multiple alleles into multiple records, or combine overallpoing alleles into a single record 6
VCFcheck: Verify that the reference allele matches the reference genome 6
VCFcombine: Combine multiple VCF datasets 7
VCFcommonSamples: Output records belonging to samples common between two datasets 6
VCFdistance: Calculate distance to the nearest variant 6
VCFfilter: filter VCF data in a variety of attributes 6
VCFfixup: Count the allele frequencies across alleles present in each record in the VCF file 5
VCFflatten: Removes multi-allelic sites by picking the most common alternate 5
VCFgenotype-to-haplotype: Convert genotype-based phased alleles into haplotype alleles 7
VCFgenotypes: Convert numerical representation of genotypes to allelic 6
VCFhetHomAlleles: Count the number of heterozygotes and alleles, compute het/hom ratio 6
VCFleftAlign: Left-align indels and complex variants in VCF dataset 6
VCFprimers: Extract flanking sequences for each VCF record 5
VCFrandomSample: Randomly sample sites from VCF dataset 7
VCFselectsamples: Select samples from a VCF dataset 7
VCFsort: Sort VCF dataset by coordinate 5
VCFtoTab-delimited: Convert VCF data into TAB-delimited format 8
vectorstrip Strips out DNA between a pair of vector sequences 4
Venn Generate Venn diagrams for groups 5
Venn diagram [JVenn] 3
VSearch alignment Chimeric sequence detection Sequence clustering Sequence masking 5
VSearch chimera detection Chimeric sequence detection Sequence clustering Sequence masking 5
VSearch clustering Chimeric sequence detection Sequence clustering Sequence masking 6
VSearch dereplication Chimeric sequence detection Sequence clustering Sequence masking 6
VSearch masking Chimeric sequence detection Sequence clustering Sequence masking 5
VSearch search Chimeric sequence detection Sequence clustering Sequence masking 5
VSearch shuffling Chimeric sequence detection Sequence clustering Sequence masking 5
VSearch sorting Chimeric sequence detection Sequence clustering Sequence masking 6
water Smith-Waterman local alignment 4
Wig/BedGraph-to-bigWig converter 2
Wiggle to Interval 1
Wiggle-to-Interval converter 1
WindowBed find overlapping intervals within a window around an interval 17
wobble Wobble base plot 4
wordcount Counts words of a specified size in a DNA sequence 4
wordmatch Finds all exact matches of a given size between 2 sequences 4
xcms adjustRtime (retcor) Retention Time Correction 9
xcms fillChromPeaks (fillPeaks) Integrate areas of missing peaks 10
xcms findChromPeaks (xcmsSet) Chromatographic peak detection 12
xcms findChromPeaks Merger Merge xcms findChromPeaks RData into a unique file to be used by group 4
xcms get a sampleMetadata file which need to be filled with extra information 1
xcms groupChromPeaks (group) Perform the correspondence, the grouping of chromatographic peaks within and between samples. 10
xcms plot chromatogram Plots base peak intensity chromatogram (BPI) and total ion current chromatogram (TIC) from MSnbase or xcms experiment(s) 2
xcms process history Create a summary of XCMS analysis 7