Examples : samtools, bed, topic:conversion

190 tool(s) found

Tool Description Topics Available version(s)
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