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perl-version
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public |
Structured version objects
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2025-03-25 |
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perl-text-abbrev
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public |
abbrev - create an abbreviation table from a list
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2025-03-25 |
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perl-cpan-meta-yaml
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public |
Read and write a subset of YAML for CPAN Meta files
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2025-03-25 |
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perl-json-pp
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public |
JSON::XS compatible pure-Perl module.
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2025-03-25 |
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arboreto
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public |
Scalable gene regulatory network inference using tree-based ensemble regressors
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2025-03-25 |
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sequencetools
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public |
A tool (pileupCaller) for processing ancient DNA sequencing data
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2025-03-25 |
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mauve
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public |
Mauve is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion
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2025-03-25 |
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perl-storable
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public |
persistence for Perl data structures
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2025-03-25 |
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grid
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public |
Growth Rate Index (GRiD) measures bacterial growth rate from reference genomes (including draft quality genomes) and metagenomic bins at ultra-low sequencing coverage (> 0.2x).
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2025-03-25 |
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itsxpress
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public |
ITSxpress: Software to rapidly trim the Internally Transcribed Spacer (ITS) region from FASTQ files.
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2025-03-25 |
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icount
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public |
Computational pipeline for analysis of iCLIP data
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2025-03-25 |
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biopet-basecounter
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public |
BaseCounter counts the bases from genes and transcripts and outputs information on the counts in exonic and intronic regions as well as information on the counts on the sense and antisense strands.
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2025-03-25 |
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sshmm
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public |
ssHMM is an RNA motif finder that recovers sequence-structure motifs from RNA-binding protein data, such as CLIP-Seq data.
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2025-03-25 |
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gbsx
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public |
Toolkit for experimental design and demultiplexing genotyping by sequencing experiments
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2025-03-25 |
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anndata
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public |
An annotated data matrix.
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2025-03-25 |
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regtools
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public |
Tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context.
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2025-03-25 |
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alignstats
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public |
Comprehensive alignment, whole-genome coverage, and capture coverage statistics.
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2025-03-25 |
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biopet-seattleseqkit
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public |
#### Tool - Filter This tool can filter a seattle seq file.
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2025-03-25 |
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mauvealigner
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public |
The mauveAligner and progressiveMauve command-line tools for generating multiple genome alignments in the presence of large-scale evolutionary events
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2025-03-25 |
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phenix
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public |
Public Health England SNP calling pipeline
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2025-03-25 |
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metaquant
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public |
Quantitative microbiome analysis
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2025-03-25 |
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scvi
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public |
Single-cell Variational Inference
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2025-03-25 |
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perl-string-random
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public |
Perl module to generate random strings based on a pattern
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2025-03-25 |
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libmems
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public |
libMems is a freely available software development library to support DNA string matching and comparative genomics.
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2025-03-25 |
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ucsc-bedjointaboffset
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public |
given a bed file and tab file where each have a column with matching values: first get the value of column0, the offset and line length from inTabFile. Then go over the bed file, use the name field and append its offset and length to the bed file as two separate fields. Write the new bed file to outBed.
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2025-03-25 |
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ucsc-endsinlf
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public |
Check that last letter in files is end of line
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2025-03-25 |
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ucsc-gensub2
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public |
version 12.18
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2025-03-25 |
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ucsc-hgloadsqltab
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public |
Load table into database from SQL and text files.
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2025-03-25 |
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ucsc-para
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public |
version 12.18
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2025-03-25 |
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ucsc-parahub
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public |
parasol hub server version 12.18
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2025-03-25 |
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ucsc-parahubstop
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public |
version 12.18
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2025-03-25 |
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ucsc-paranode
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public |
version 12.18
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2025-03-25 |
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ucsc-paranodestart
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public |
version 12.18
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2025-03-25 |
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ucsc-paranodestatus
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public |
version 12.18
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2025-03-25 |
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ucsc-paranodestop
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public |
Shut down parasol node daemons on a list of machines
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2025-03-25 |
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ucsc-parasol
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public |
Parasol is the name given to the overall system for managing jobs on a computer cluster and to this specific command. This command is intended primarily for system administrators. The 'para' command is the primary command for users.
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2025-03-25 |
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ucsc-paratestjob
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public |
version 12.18
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2025-03-25 |
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ucsc-pslsomerecords
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public |
Extract multiple psl records
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2025-03-25 |
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ucsc-websync
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public |
download from https server, using files.txt on their end to get the list of files
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2025-03-25 |
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libgenome
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public |
A C++ development library designed to make common operations on DNA and protein sequences easy. libGenome provides functionality to read, write, and manipulate sequence and annotation data in several file formats.
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2025-03-25 |
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biopet-fastqsplitter
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public |
This tool divides a fastq file into smaller fastq files, based on the number of output files specified.
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2025-03-25 |
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pmdtools
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public |
Compute postmortem damage patterns and decontaminate ancient genomes
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2025-03-25 |
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r-phewas
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public |
Phenome Wide Association Studies (PheWAS) - Functions to perform Phenome Wide Association Studies (PheWAS). These functions include the conversion of ICD9 codes to PheWAS codes (v1.2), statistical analysis, and plotting.
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2025-03-25 |
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biopet-scatterregions
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public |
This tool breaks a reference or bed file into smaller scatter regions of equal size.
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2025-03-25 |
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pasa
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public |
PASA, acronym for Program to Assemble Spliced Alignments (and pronounced 'pass-uh'), is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures, and to maintain gene structure annotation consistent with the most recently available experimental sequence data. PASA also identifies and classifies all splicing variations supported by the transcript alignments.
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2025-03-25 |
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atactk
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public |
A toolkit for working with ATAC-seq data.
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2025-03-25 |
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fastphylo
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public |
Fastphylo is software project containing the implementations of the algorithms "Fast Computation of Distance Estimators" and "Fast Neighbor Joining".
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2025-03-25 |
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biopet-validatefastq
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public |
This tool validates a FASTQ file.
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2025-03-25 |
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heinz
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public |
The algorithm for identification of the optimal scoring subnetwork.
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2025-03-25 |
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perl-mce-shared
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public |
MCE extension for sharing data supporting threads and processes
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2025-03-25 |
