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eqtlbma
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public |
Package to detect eQTLs jointly in multiple subgroups (e.g. tissues) via Bayesian Model Averaging.
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2023-06-16 |
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perl-io-handle
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public |
supply object methods for I/O handles
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2023-06-16 |
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perl-extutils-parsexs
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public |
converts Perl XS code into C code
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2023-06-16 |
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motus
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public |
Marker gene-based OTU (mOTU) profiling
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2023-06-16 |
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basic
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public |
BASIC is a semi-de novo assembly method for assembling BCR and TCR genes from single cell RNA-seq data.
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2023-06-16 |
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perl-xsloader
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public |
Dynamically load C libraries into Perl code
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2023-06-16 |
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ngless
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public |
A tool for short-read processing with a focus on metagenomics
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2023-06-16 |
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flapjack
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public |
Flapjack provides interactive visualizations of high-throughput genotyping data.
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2023-06-16 |
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nanosv
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public |
Structural variation detection tool for Oxford Nanopore data.
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2023-06-16 |
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behst
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public |
BEHST reads an input dataset of chromosome regions, and intersects them with the chromatin interactions available in the Hi-C dataset. Of these chromosome regions, BEHST selects those that are presentthe regulatory regions of genes of APPRIS, a dataset of principal isoform annotations. We defined these cis-regulatory regions upon the position of their nearest transcription start site of the APPRIS genes' principal transcripts (obtained through GENCODE), plus an upstream and downstream extension. Afterwards, BEHST takes the genes of the resulting partner loci found in gene regulatory regions, and performs a gene set enrichment analysis on them through g:Profiler. BEHST, finally, outputs the list of the most significant Gene Ontology terms detected by g:Profiler. Citation: Davide Chicco, Haixin Sarah Bi, Juri Reimand, and Michael M. Hoffman, 'BEHST: Genomic set enrichment analysis enhanced through integration of chromatin long-range interactions', 2018. In preparation. Website: http://behst.hoffmanlab.org/
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2023-06-16 |
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xyalign
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public |
Command line tools and python library to infer ploidy, correct for sex chromosome complement, and work with NGS data
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2023-06-16 |
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pypiper
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public |
Pypiper is a lightweight python toolkit that helps you write slick pipelines in python.
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2023-06-16 |
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pymvpa
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public |
PyMVPA -- Multivariate Pattern Analysis in Python
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2023-06-16 |
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slncky
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public |
slncky is a tool for lncRNA discovery from RNA-Seq data. slncky filters a high-quality set of noncoding transcripts, discovers lncRNA orthologs, and characterizes conserved lncRNA evolution. slncky was developed as a collaboration between the Garber Lab at UMass Medical and the Regev Lab at the Broad Institute.
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2023-06-16 |
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udocker
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public |
Freely available tools for computational molecular biology.
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2023-06-16 |
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dammit
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public |
simple de novo transcriptome annotator
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2023-06-16 |
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berokka
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public |
Trim, circularise and orient long read bacterial genome assemblies.
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2023-06-16 |
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bcl2fastq-nextseq
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public |
NextSeq .bcl Conversion
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2023-06-16 |
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python-cluster
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public |
python-cluster is a "simple" package that allows to create several groups (clusters) of objects from a list
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2023-06-16 |
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tgt
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public |
TextGridTools -- Read, write, and manipulate Praat TextGrid files
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2023-06-16 |
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orfm
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public |
OrfM is a simple and not slow ORF caller
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2023-06-16 |
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besst
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public |
Scaffolder for genomic assemblies.
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2023-06-16 |
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loompy
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public |
Work with .loom files for single-cell RNA-seq data
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2023-06-16 |
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scoary
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public |
Microbial pan-GWAS using the output from Roary
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2023-06-16 |
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afterqc
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public |
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data. AfterQC can simply go through all fastq files in a folder and then output three folders: good, bad and QC folders, which contains good reads, bad reads and the QC results of each fastq file/pair. Currently it supports processing data from HiSeq 2000/2500/3000/4000, Nextseq 500/550, MiniSeq...and other Illumina 1.8 or newer formats.
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2023-06-16 |
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blasr
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public |
No Summary
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2023-06-16 |
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blasr_libcpp
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public |
blasr_libcpp is a support library used by blasr and other PacBio tools
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2023-06-16 |
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export2graphlan
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public |
Conversion software tool for annotating tree with GraPhlAn
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2023-06-16 |
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canvas
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public |
Copy number variant (CNV) calling from DNA sequencing data
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2023-06-16 |
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metaphlan2
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public |
Metagenomic Phylogenetic Analysis
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2023-06-16 |
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ont-tombo
|
public |
Detection of modified bases from raw nanopore sequencing data.
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2023-06-16 |
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qiime
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public |
Quantitative Insights Into Microbial Ecology
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2023-06-16 |
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netreg
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public |
netReg fits linear regression models using network-penalization.
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2023-06-16 |
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secapr
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public |
Process sequence-capture FASTQ files into alignments for phylogenetic analyses. Integrates allele phasing.
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2023-06-16 |
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bwameth
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public |
A fast and accurate aligner of BS-seq reads
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2023-06-16 |
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minced
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public |
MinCED - Mining CRISPRs in Environmental Datasets
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2023-06-16 |
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jannovar-cli
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public |
Java tool for performing annotation of VCF files
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2023-06-16 |
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tracer
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public |
Tracer is a program for analysing the trace files generated by Bayesian MCMC runs (that is, the continuous parameter values sampled from the chain). It can be used to analyse runs of BEAST, MrBayes, LAMARC and possibly other MCMC programs.
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2023-06-16 |
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quasitools
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public |
Quasitools is a collection of tools for analysing Viral Quasispecies
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2023-06-16 |
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qorts
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public |
QoRTs toolkit for analysis, quality control, and data management of RNA-Seq
datasets.
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2023-06-16 |
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seqmagick
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public |
Tools for converting and modifying sequence files from the command-line
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2023-06-16 |
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discasm
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public |
DISCASM aims to extract reads that map to reference genomes in a discordant fashion and optionally include reads that do not map to the genome at all, and perform a de novo transcriptome assembly of these reads. DISCASM relies on the output from STAR (as run via STAR-Fusion), and supports de novo transcriptome assembly using Trinity or Oases. - https://github.com/DISCASM/DISCASM/wiki
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2023-06-16 |
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phylowgs
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public |
Application for inferring subclonal composition and evolution from whole-genome sequencing data
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2023-06-16 |
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kat
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public |
KAT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts
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2023-06-16 |
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mobster
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public |
NGS tool for detecting MEI and gene retrotransposition events in WGS and WES data, see Thung et al. Genome Biol. 2014 for more information.
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2023-06-16 |
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metfrag
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public |
MetFrag is a freely available software for the annotation of high precision tandem mass spectra of metabolites which is a first and critical step for the identification of a molecular structure. Candidate molecules of different databases are fragmented in silico and matched against mass to charge values. A score calculated using the fragment peak matches gives hints to the quality of the candidate spectrum assignment.
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2023-06-16 |
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ribocode
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public |
A package for detecting the actively translated ORFs using ribosome-profiling data
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2023-06-16 |
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prosolo
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public |
A highly sensitive and accurate Bayesian caller for variants in single cell sequencing data.
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2023-06-16 |
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perl-module-load-conditional
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public |
Looking up module information / loading at runtime
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2023-06-16 |
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edlib
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public |
C/C++ library and program for sequence alignment using edit (Levenshtein) distance
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2023-06-16 |
