182 tool(s) found

Tool Description Topics Available version(s)
AddCommentsToBam add comments to BAM dataset 14
AddOrReplaceReadGroups add or replaces read group information 14
Annotate DESeq2/DEXSeq output tables Append annotation from GTF to differential expression tool outputs 2
Bar chart for multiple columns 2
BED-to-bigBed converter Conversion 2
BedToIntervalList convert coordinate data into picard interval list format 14
bedtools BAM to BED converter 23
bedtools Multiple Intersect identifies common intervals among multiple interval files 23
Bismark bisulfite mapper (bowtie) 2
Bismark Mapper Bisulfite reads mapper 15
Bismark Meth. Extractor Reports on methylation status of reads mapped by Bismark 11
Boxplot of quality statistics 2
BSMAP Mapper 1
BSMAP Methylation Caller 1
bwameth Fast and accurate aligner of BS-Seq reads. 6
Change Case of selected columns 2
CleanSam perform SAM/BAM grooming 14
CML to InChI 3
CML to mol2 3
CML to SDF 3
CML to SMILES 3
Collect Alignment Summary Metrics writes a file containing summary alignment metrics 14
CollectBaseDistributionByCycle charts the nucleotide distribution per cycle in a SAM or BAM dataset 14
CollectGcBiasMetrics charts the GC bias metrics 14
CollectInsertSizeMetrics plots distribution of insert sizes 14
CollectRnaSeqMetrics collect metrics about the alignment of RNA to various functional classes of loci in the genome 14
CollectWgsMetrics compute metrics for evaluating of whole genome sequencing experiments 14
Concat fasta files Concatenates fasta files you select from your history 1
Concatenate multiple datasets tail-to-head 4
Convert BED to Feature Location Index 1
Convert BED to GFF 2
Convert FASTA to 2bit 2
Convert FASTA to Bowtie base space Index 2
Convert FASTA to Bowtie color space Index 2
Convert FASTA to len file 2
Convert FASTA to Tabular 1
Convert genome coordinates between assemblies and genomes 2
Convert Genomic Intervals To BED 1
Convert Genomic Intervals To Coverage 2
Convert Genomic Intervals To Strict BED 2
Convert Genomic Intervals To Strict BED12 1
Convert Genomic Intervals To Strict BED6 2
Convert GFF to BED 2
Convert GFF to Feature Location Index 1
Convert Len file to Linecount 2
Convert lped to fped 2
Convert lped to plink pbed 2
Convert MAF to Fasta 2
Convert MAF to Genomic Intervals 2
Convert Picard Interval List to BED6 converter 2
Convert plink pbed to ld reduced format 2
Convert plink pbed to linkage lped 2
Convert Ref taxonomy to Seq Taxonomy converts 2 or 3 column sequence taxonomy file to a 2 column mothur taxonomy_outline format 2
Convert SAM to BAM 1
Convert tabular to dbnsfp 2
Count occurrences of each record 2
Count intervals in one file overlapping intervals in another file 2
Create a BedGraph of genome coverage 3
Create a histogram of genome coverage 3
Cut columns from a table Filtering 2
cut_francais keep or remove selected column 1
Data Fetch Query and retrieval 1
DESeq2 Determines differentially expressed features from count tables Differential gene expression profiling RNA-Seq quantification 21
Downsample SAM/BAM Downsample a file to retain a subset of the reads 14
EstimateLibraryComplexity assess sequence library complexity from read sequences 14
Extract Genomic DNA using coordinates from assembled/unassembled genomes 7
Extract MAF blocks given a set of genomic intervals 3
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
FASTQ Dump paired downloader Downloads a set of paired reads by their accession number using fastq-dump tool from sra-toolkit. 1
FASTQ Groomer convert between various FASTQ quality formats Sequence conversion 5
FASTQ Trimmer by column Sequence trimming 5
FastQC Read Quality reports Sequence composition calculation Sequencing quality control Statistical calculation 18
FastqToSam convert Fastq data into unaligned BAM 18
featureCounts Measure gene expression in RNA-Seq experiments from SAM or BAM files. Sequence assembly 25
Filter data on any column using simple expressions Formatting 2
Filter GFF data by attribute using simple expressions 3
Filter MAF by specified attributes 1
Filter MAF blocks by Size 1
Filter MAF blocks by Species 1
FilterSamReads include or exclude aligned and unaligned reads and read lists 14
FixMateInformation ensure that all mate-pair information is in sync between each read and it's mate pair 14
GATK tool collection Version 3.4-0 2
Gene BED To Exon/Intron/Codon BED expander 1
Gene length and GC content from GTF and FASTA file 4
Genomic imprinting Detection pipeline based on Hardy-Weinberg equilibrium 1
Get Microbial Data Query and retrieval 1
goseq tests for overrepresented gene categories Gene-set enrichment analysis 10
Group data by a column and perform aggregate operation on other columns. 4
heatmap2 4
htseq-count - Count aligned reads in a BAM file that overlap features in a GFF file 9
InChI to CML 3
InChI to MOL 3
InChI to MOL2 3
InChI to SDF 3
InChI to SMILES 3
Infinium Analysis Infinium Analysis 1
Intersect BAM alignments with intervals in another files 2
Join MAF blocks by Species 1
Join two Datasets side by side on a specified field 4
Line/Word/Character count of a dataset 1
MAF Coverage Stats Alignment coverage information 3
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
Map with Bowtie for Illumina 7
Map with BWA for Illumina 1
Map with BWA for SOLiD 1
MarkDuplicates examine aligned records in BAM datasets to locate duplicate molecules 15
MarkDuplicatesWithMateCigar examine aligned records in BAM datasets to locate duplicate molecules 14
MeanQualityByCycle chart distribution of base qualities 14
Merge BedGraph files 3
MergeBamAlignment merge alignment data with additional info stored in an unmapped BAM dataset 14
MergeSamFiles merges multiple SAM/BAM datasets into one 14
MOL to CML 3
MOL to MOL2 3
MOL to SMILES 3
MOL2 to CML 3
MOL2 to InChI 3
MOL2 to MOL 3
MOL2 to SDF 3
MOL2 to SMILES 3
mQC quality control of ribosome profiling mapping results 2
NormalizeFasta normalize fasta datasets 14
Paste two files side by side 1
Peptide Shaker Perform protein identification using various search engines based on results from SearchGUI 19
proBAMconvert peptide identifications to proBAM or proBED 1
QualityScoreDistribution chart quality score distribution 14
ReorderSam reorder reads to match ordering in reference sequences 17
ReplaceSamHeader replace header in a SAM/BAM dataset 17
Reverse Complement a MAF file 1
RevertOriginalBaseQualitiesAndAddMateCigar revert the original base qualities and add the mate cigar tag 14
RevertSam revert SAM/BAM datasets to a previous state 14
RNA STAR Gapped-read mapper for RNA-seq data Mapping assembly Sequence alignment 17
RNAseq Analysis by combination of various filtering, normalization and DE analysis methods 1
SamToFastq extract reads and qualities from SAM/BAM dataset and convert to fastq 18
Samtools fastx extract FASTA or FASTQ from alignment files 2
SDF to CML 3
SDF to InChI 3
SDF to mol2 3
SDF to SMILES 3
Search GUI Perform protein identification using various search engines and prepare results for input to Peptide Shaker 22
Select last lines from a dataset 2
Select random lines from a file 2
SFF converter 1
Sickle windowed adaptive trimming of FASTQ data 4
SMILES to CML 3
SMILES to InChI 3
SMILES to MOL 3
SMILES to MOL2 3
SMILES to SDF 3
SMILES to SMILES 3
Sort data in ascending or descending order 3
SortSam sort SAM/BAM dataset 14
Split MAF blocks by Species 1
Step 1: Mapping (can be both RIBO-seq or RNA-seq) using fastq files as input 1
Step 2: MappingQC quality control of mapping results 1
Step 3: TIS calling Finds all TISes in your ribosome profiling data. 1
Step 3: Transcript calling for all ribosome profiles 1
Step 4: TIS overview Create a tab separated file from the TIS_overview table. 1
Step 5: SNP calling using mapped next-generation sequencing reads 1
Step 6: Translation assembly Assembles all translation products 1
Step 7: Translation Database Generates a Translation Product database 1
Step 8: FLOSS calculation Calculates first (if not already done for that analysis id) the reference fractions and cut off values based on known protein-coding transcripts. With these, the FLOSS scores are calculated and classified for each possible translation product. 1
Stitch Gene blocks given a set of coding exon intervals 4
Stitch MAF blocks given a set of genomic intervals 1
Summary Statistics for any numerical column 3
Table Compute computes operations on table data 3
TopHat Gapped-read mapper for RNA-seq data 9
Tophat for Illumina Find splice junctions using RNA-seq data 2
Trim leading or trailing characters 2
UMI-tools count performs quantification of UMIs from BAM files 9
UMI-tools deduplicate Extract UMI from fastq files 6
UMI-tools extract Extract UMI from fastq files 12
UMI-tools group Extract UMI from fastq files 8
UMI-tools whitelist Extract cell barcodes from FASTQ files 8
Upload File from your computer Query and retrieval 3
ValidateSamFile assess validity of SAM/BAM dataset 14
VCF to MAF Custom Track for display at UCSC 2
WIG parser 1
Wig/BedGraph-to-bigWig converter 2
Wiggle to Interval 2