168 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] 4
Add protein features [neXtProt, Human] 6
Add protein features [UniProt, Human, Mouse, Rat] 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
BED-to-bigBed converter Conversion 2
BED-to-GFF converter Conversion 1
Biological theme comparison (Human, Mouse, Rat)[clusterProfiler] 4
Boxplot of quality statistics 2
Build Protein interaction network [BioGRID, BioPlex, HuMAP] 2
Build tissue-specific expression dataset [Human Protein Atlas] 5
Change Case of selected columns 1
Classification and enrichment analysis (Human, Mouse, Rat)[clusterProfiler] 1
CML to InChI 2
CML to mol2 2
CML to SDF 2
CML to SMILES 2
Compare two Datasets to find common or distinct rows 1
Compute an expression on every row 4
Compute functional profiles (Human, Mouse) [goProfiles] 5
Concatenate datasets tail-to-head (cat) 7
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 2
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 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 without sorting 1
Convert tabular to CSV 1
Convert tabular to dbnsfp 2
Convert tar to directory 2
Convert uncompressed BCF to BCF 1
Count occurrences of each record 2
Create single interval as a new dataset 1
Create text file with recurring lines 8
CustomProDB Generate protein FASTAs from exosome or transcriptome data 2
Cut columns from a table (cut) 8
Data Fetch 1
Enrichment analysis (Human, Mouse, Rat)[topGO] 2
Extract features from GFF data 1
Extract Genomic DNA using coordinates from assembled/unassembled genomes 8
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 and/or numerical value 7
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 profiles by (normal or tumor) tissue/cell type [Human Protein Atlas] 3
Get MS/MS observations in tissue/fluid [Human Peptide Atlas] 7
Get unique peptide SRM-MRM method [Human SRM Atlas] 2
GFF-to-BED converter Conversion 1
Group data by a column and perform aggregate operation on other columns. 5
GTF-to-BEDGraph converter Conversion 1
HeatMap (clustering and visualization) 6
ID Converter (Human, Mouse, Rat) 1
InChI to CML 2
InChI to MOL 2
InChI to MOL2 2
InChI to SDF 2
InChI to SMILES 2
Join two files 10
Join MAF blocks by Species 1
Join two Datasets side by side on a specified field 4
KEGG pathways mapping and coverage [PathView] 4
KEGG pathways mapping and visualization [PathView] 7
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
Multi-Join (combine multiple files) 8
Paste two files side by side 1
Pathway enrichment analysis [Reactome] 5
Peptide Shaker Perform protein identification using various search engines based on results from SearchGUI 12
Protein Database Downloader 2
PSM to SAM Generate SAM files from PSMs. 1
QuanTP Correlation between protein and transcript abundances 2
Remove beginning of a file 1
Replace parts of text 9
Replace Text in entire line 8
Replace Text in a specific column 8
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 15
Search in textfiles (grep) 7
Secure Hash / Message Digest on a dataset 2
Select lines that match an expression 1
Select first lines from a dataset (head) 8
Select first lines from a dataset 1
Select last lines from a dataset (tail) 8
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 7
Sort data in ascending or descending order 2
Sort a row according to their columns 8
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) 8
Text reformatting with awk 7
Text transformation with sed 7
Trim leading or trailing characters 1
Unfold columns from a table 7
Unique occurrences of each record 8
Unique lines assuming sorted input file 7
Upload File from your computer 2
VCF to MAF Custom Track for display at UCSC 2
Venn diagram [JVenn] 6
Volcano Plot create a volcano plot 3
Wig/BedGraph-to-bigWig converter 2
Wiggle to Interval 2
Wiggle-to-Interval converter 2