165 tool(s) found

Tool Description Topics Available version(s)
Add column to an existing dataset 3
Add expression data to your protein list mRNA and protein level data from Human Protein Atlas 1
AXT to concatenated FASTA Converts an AXT formatted file to a concatenated FASTA alignment Conversion 1
AXT to FASTA Converts an AXT formatted file to FASTA format Conversion 1
AXT to LAV Converts an AXT formatted file to LAV format Conversion 1
Bar chart for multiple columns 1
bcftools call SNP/indel variant calling from VCF/BCF 6
bcftools mpileup Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files 2
bcftools view VCF/BCF conversion, view, subset and filter VCF/BCF files 9
BED-to-bigBed converter Conversion 2
BED-to-GFF converter Conversion 1
Boxplot of quality statistics 1
Change Case of selected columns 1
clusterProfiler GO terms classification and enrichment analysis 2
CML to InChI 2
CML to mol2 2
CML to SDF 2
CML to SMILES 2
Column Regex Find And Replace 3
Compare two Datasets to find common or distinct rows 1
Compute an expression on every row 3
Concat fasta files Concatenates fasta files you select from your history 1
Concatenate datasets tail-to-head (cat) 5
Concatenate datasets tail-to-head 1
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 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 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 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 BAM without sorting 1
Convert tabular to dbnsfp 1
Convert uncompressed BCF to BCF 1
Count occurrences of each record 1
Create single interval as a new dataset 1
Create text file with recurring lines 6
CustomProDB Generate protein FASTAs from exosome or transcriptome data 1
Cut columns from a table (cut) 6
Cut columns from a table 2
Data Fetch 1
Extract features from GFF data 1
Extract Genomic DNA using coordinates from assembled/unassembled genomes 7
Extract MAF blocks given a set of genomic intervals 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
FASTA Merge Files and Filter Unique Sequences Concatenate FASTA database files together 3
Filter data on any column using simple expressions Formatting 1
Filter by keywords or numerical value 1
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 MAF by specified attributes 1
Filter MAF blocks by Size 1
Filter MAF blocks by Species 1
Gene BED To Exon/Intron/Codon BED expander 1
Get expression data by tissue finds tissue in which your proteins are expressed (or not) - Human Protein Atlas 1
GFF-to-BED converter Conversion 1
goProfiles Statistical analysis of functional profiles 2
Group data by a column and perform aggregate operation on other columns. 2
GTF-to-BEDGraph converter Conversion 1
ID Converter convert public database identifiers 2
InChI to CML 2
InChI to MOL 2
InChI to MOL2 2
InChI to SDF 2
InChI to SMILES 2
Join two files 7
Join MAF blocks by Species 1
Join two Datasets side by side on a specified field 2
JVenn diagram processes lists and produces Venn diagrams 2
KEGG pathways coverage 1
LAV to BED Converts a LAV formatted file to BED format 1
Line/Word/Character count of a dataset 1
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
Merge Columns together 2
MOL to CML 2
MOL to MOL2 2
MOL to SMILES 2
MOL2 to CML 2
MOL2 to InChI 2
MOL2 to MOL 2
MOL2 to SDF 2
MOL2 to SMILES 2
MPileup call variants 10
Multi-Join (combine multiple files) 6
Paste two files side by side 1
Peptide Shaker Perform protein identification using various search engines based on results from SearchGUI 10
Protein Database Downloader 2
Protein features add biochemical and cellular annotation to your protein list from neXtProt 1
PSM to SAM Generate SAM files from PSMs. 1
Reactome queries web service and display pathways 1
Regex Find And Replace 2
Remove beginning of a file 1
Replace parts of text 6
Replace Text in entire line 6
Replace Text in a specific column 6
Retrieve number of MS/MS observations in a tissue from Peptide Atlas – homo sapiens only 1
Retrieve tissue-specific expression data from HPA (Human Protein Atlas) - no input required 1
Reverse Complement a MAF file 1
SDF to CML 2
SDF to InChI 2
SDF to mol2 2
SDF to SMILES 2
Search GUI Perform protein identification using various search engines and prepare results for input to Peptide Shaker 12
Search in textfiles (grep) 6
Secure Hash / Message Digest on a dataset 1
Select lines that match an expression 1
Select first lines from a dataset 1
Select first lines from a dataset (head) 6
Select last lines from a dataset (tail) 6
Select last lines from a dataset 1
Select random lines from a file 2
SFF converter 1
SMILES to CML 2
SMILES to InChI 2
SMILES to MOL 2
SMILES to MOL2 2
SMILES to SDF 2
SMILES to SMILES 2
Sort data in ascending or descending order 6
Sort data in ascending or descending order 2
Sort a row according to their columns 6
Split MAF blocks by Species 1
Stitch Gene blocks given a set of coding exon intervals 1
Stitch MAF blocks given a set of genomic intervals 1
Summary Statistics for any numerical column 3
tac reverse a file (reverse cat) 6
Text reformatting with awk 6
Text transformation with sed 6
topGO Enrichment analysis for Gene Ontology 2
Trim leading or trailing characters 1
Unfold columns from a table 6
Unique occurrences of each record 6
Unique lines assuming sorted input file 6
Upload File from your computer 2
VCF to MAF Custom Track for display at UCSC 1
Wig/BedGraph-to-bigWig converter 2
Wiggle to Interval 1
Wiggle-to-Interval converter 1