Add column |
to an existing dataset |
|
3 |
Aggregate datapoints |
Appends the average, min, max of datapoints per interval |
|
2 |
BamLeftAlign |
indels in BAM datasets |
|
8 |
bcftools call |
SNP/indel variant calling from VCF/BCF |
|
9 |
bed to protein map |
genomic location of proteins for MVP |
|
1 |
BED-to-bigBed |
converter |
Conversion
|
2 |
BED-to-GFF |
converter |
Conversion
|
1 |
BLAST XML to selected tabular columns |
Convert BLAST XML output to tabular |
|
1 |
BLAST XML to tabular |
Convert BLAST XML output to tabular |
Conversion
|
16 |
Change Case |
of selected columns |
|
1 |
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 |
|
4 |
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 gffCompare annotated GTF to BED |
for StringTie results |
|
2 |
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 |
CRAVAT Convert |
Converts a VCF format file to a Cravat format file |
|
1 |
CRAVAT Query |
Queries CRAVAT for cancer annotation |
|
1 |
CRAVAT Submit, Check, and Retrieve |
Submits, checks for, and retrieves data for cancer annotation |
|
1 |
CRAVAT-P Submit, Intersect, Check, and Retrieve |
| Submits, intersects, checks for, and retrieves data for cancer annotation. |
|
1 |
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 |
Cut |
columns from a table |
|
2 |
Data Fetch |
|
|
1 |
DAVID |
functional annotation for a list of genes |
|
1 |
Extract features |
from GFF data |
|
1 |
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 |
FASTA-to-Tabular |
converter |
|
4 |
Filter |
data on any column using simple expressions |
Formatting
|
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 |
Filter sequences by length |
|
Filtering
|
7 |
Filter Tabular |
|
|
3 |
FreeBayes |
bayesian genetic variant detector |
|
8 |
g:Profiler |
tools for functional profiling of gene lists |
|
1 |
Gene BED To Exon/Intron/Codon BED |
expander |
|
1 |
GFF-to-BED |
converter |
Conversion
|
1 |
GffCompare |
compare assembled transcripts to a reference annotation |
|
5 |
Group |
data by a column and perform aggregate operation on other columns. |
|
5 |
HISAT2 |
A fast and sensitive alignment program |
|
17 |
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 |
LD |
linkage disequilibrium and tag SNPs |
|
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 |
MasterVar to pgSnp |
Convert from MasterVar to pgSnp 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 |
msconvert |
Convert and filter a mass spec peak list |
|
2 |
Multi-Join |
(combine multiple files) |
|
8 |
mz to sqlite |
Extract mzIdentML and associated proteomics datasets into a SQLite DB |
|
2 |
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
|
13 |
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
|
11 |
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
|
13 |
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 |
Paste |
two files side by side |
|
1 |
PepPointer |
classify genomic location of peptides |
|
1 |
Peptide Genomic Coodinate |
Get Peptide's genomic coordinate using mzsqlite DB and genomic mapping sqlite DB |
|
1 |
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 |
Query Tabular |
using sqlite sql |
|
8 |
Regex Find And Replace |
|
|
2 |
Remove beginning |
of a file |
|
1 |
Replace |
parts of text |
|
9 |
Replace Text |
in a specific column |
|
8 |
Replace Text |
in entire line |
|
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 |
|
1 |
Select last |
lines from a dataset (tail) |
|
8 |
Select random lines |
from a file |
|
2 |
Send to cloud |
|
|
1 |
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 |
SQLite to tabular |
for SQL query |
|
4 |
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 |
Summary Statistics |
for any numerical column |
|
3 |
Tabular-to-FASTA |
converts tabular file to FASTA format |
|
3 |
tac |
reverse a file (reverse cat) |
|
8 |
Text reformatting |
with awk |
|
7 |
Text transformation |
with sed |
|
7 |
TopHat |
Gapped-read mapper for RNA-seq data |
|
10 |
Translate BED transcripts |
cDNA in 3frames or CDS |
|
1 |
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 |
Wig/BedGraph-to-bigWig |
converter |
|
2 |
Wiggle to Interval |
|
|
2 |
Wiggle-to-Interval |
converter |
|
2 |