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fastani
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public |
FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI).
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2025-03-25 |
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evidencemodeler
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public |
Evidence Modeler combines ab intio gene predictions, protein alignments, and transcript alignments into weighted consensus gene structures
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2025-03-25 |
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biolib
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public |
Package for common tasks in bioinformatics.
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2025-03-25 |
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kraken2
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public |
Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.
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2025-03-25 |
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smeg
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public |
Strain-level Metagenomic Estimation of Growth rate (SMEG) measures growth rates of microbial strains from complex metagenomic dataset
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2025-03-25 |
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cgatcore
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public |
CGAT : the Computational Genomics Analysis Toolkit
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2025-03-25 |
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dadi
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public |
Fit population genetic models using diffusion approximations to the allele frequency spectrum
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2025-03-25 |
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gdc
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public |
Utility designed for compression of genome collections from the same species.
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2025-03-25 |
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msalign2
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public |
Aligns 2 CE-MS or LC-MS datasets using accurate mass information.
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2025-03-25 |
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r-whopgenome
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public |
Provides very fast access to whole genome, population scale variation data from VCF files and sequence data from FASTA-formatted files. It also reads in alignments from FASTA, Phylip, MAF and other file formats. Provides easy-to-use interfaces to genome annotation from UCSC and Bioconductor and gene ontology data from AmiGO and is capable to read, modify and write PLINK .PED-format pedigree files.
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2025-03-25 |
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poppunk
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public |
PopPUNK (POPulation Partitioning Using Nucleotide Kmers)
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2025-03-25 |
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apt-probeset-summarize
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public |
From Affymetrix Power Tools package. apt-probeset-summarize is program for analyzing expression arrays including 3' IVT and exon arrays. Supports background correction (MAS5,RMA), normalization (linear scaling, quantile, sketch), and summarization (PLIER, RMA, MAS5) methods.
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2025-03-25 |
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duphold
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public |
SV callers like lumpy look at split-reads and pair distances to find structural variants. This tool is a fast way to add depth information to those calls.
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2025-03-25 |
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perl-snap
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public |
SNAP calculates pairwise synonymous and nonsynonymous distances according to the Nei and Gojobori method for an alignment in table format.
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2025-03-25 |
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simka
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public |
Simka and simkaMin are de novo comparative metagenomics tools. Simka represents each dataset as a k-mer spectrum and computes several classical ecological distances between them. SimkaMin outputs approximate (but very similar) results by subsampling the kmer space and requires much less computational resources.
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2025-03-25 |
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perl-autodie
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public |
Replace functions with ones that succeed or die with lexical scope
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2025-03-25 |
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topas
|
public |
This toolkit allows the efficient manipulation of sequence data in various ways. It is organized into modules: The FASTA processing modules, the FASTQ processing modules, the GFF processing modules and the VCF processing modules.
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2025-03-25 |
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reparation_blast
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public |
A pipeline that detects novel open reading frames with ribseq data for bacteria.
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2025-03-25 |
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rpf-count-cds
|
public |
A python script for counting RPF reads map to CDS region.
|
2025-03-25 |
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biopet-bamstats
|
public |
BamStats is a package that contains tools to generate stats from a BAM file, merge those stats for multiple samples, and validate the generated stats files.
|
2025-03-25 |
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scanpy
|
public |
Single-Cell Analysis in Python. Scales to >1M cells.
|
2025-03-25 |
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comparems2
|
public |
A simple tool developed to compare, globally, all MS/MS spectra between two datasets (in Mascot Generic Format or MGF).
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2025-03-25 |
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abeona
|
public |
A simple transcriptome assembler based on kallisto and Cortex graphs.
|
2025-03-25 |
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delegation
|
public |
Simple implementation of the delegate pattern.
|
2025-03-25 |
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cortexpy
|
public |
A Python API for manipulating (Mc)Cortex de novo assembly graph and link data
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2025-03-25 |
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bufet
|
public |
Tool that performs the unbiased miRNA functional enrichment analysis (Bleazard et al.) requiring significantly reduced excution times (less than 10 minutes for 1 million iterations).
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2025-03-25 |
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lightassembler
|
public |
Lightweight assembly algorithm designed to be executed on a desktop machine. It uses a pair of cache oblivious Bloom filters, one holding a uniform sample of g-spaced sequenced k-mers and the other holding k-mers classified as likely correct, using a simple statistical test.
|
2025-03-25 |
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mccortex
|
public |
De novo genome assembly and multisample variant calling
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2025-03-25 |
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thermorawfileparser
|
public |
Wrapper around the .net (C#) ThermoFisher ThermoRawFileReader library for running on Linux with mono
|
2025-03-25 |
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bandage
|
public |
Bandage - a Bioinformatics Application for Navigating De novo Assembly Graphs Easily.
|
2025-03-25 |
|
stream
|
public |
STREAM-Single-cell Trajectories Reconstruction, Exploration And Mapping
|
2025-03-25 |
|
arb-bio-devel
|
public |
ARB 6 Sequence Analysis Suite
|
2025-03-25 |
|
arb-bio-tools
|
public |
ARB 6 Sequence Analysis Suite
|
2025-03-25 |
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libarbdb
|
public |
ARB 6 Sequence Analysis Suite
|
2025-03-25 |
|
zerone
|
public |
Zerone discretizes several ChIP-seq replicates simultaneously and resolves conflicts between them.
|
2025-03-25 |
|
ghost-tree
|
public |
ghost-tree is a bioinformatics tool that combines sequence data from two
genetic marker databases into one phylogenetic tree that can be used for
diversity analyses.
|
2025-03-25 |
|
gatb
|
public |
The Genome Analysis Toolbox with de-Bruijn graph
|
2025-03-25 |
|
bioconductor-singlecellexperiment-scripts
|
public |
A set of wrappers for operations associated with the SingleCellExperiment package. Functions in R packages are hard to call when building workflows outside of R, so this package adds a set of simple wrappers with robust argument parsing. Intermediate steps are currently mainly serialized R objects, but the ultimate objective is to have language-agnostic intermediate formats allowing composite workflows using a variety of software packages.
|
2025-03-25 |
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biobb_md
|
public |
Deprecated Package: biobb_md is no longer maintained and has been superseded by the biobb_gromacs package. Biobb_md is the Biobb module collection to perform molecular dynamics simulations.
|
2025-03-25 |
|
hicmatrix
|
public |
Library to manage Hi-C matrices for HiCExplorer and pyGenomeTracks
|
2025-03-25 |
|
smcounter2
|
public |
smCounter2: an accurate low-frequency variant caller for targeted sequencing data with unique molecular identifiers
|
2025-03-25 |
|
solexaqa
|
public |
Quality statistics and visual representations for second-generation sequencing data
|
2025-03-25 |
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shannon
|
public |
A program for assembling transcripts from RNA-Seq data.
|
2025-03-25 |
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genclust
|
public |
A genetic algorithm for clustering gene expression data.
|
2025-03-25 |
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pyega3
|
public |
EGA python client
|
2025-03-25 |
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krakenuniq
|
public |
Metagenomics classifier with unique k-mer counting for more specific results
|
2025-03-25 |
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python-rnacentral
|
public |
This tool exploits the RNAcentral public APIs to automatically retrieve sequences (converted to the FASTA format) and the related metadata, starting with one or a list of RNAcentral IDs
|
2025-03-25 |
|
tigmint
|
public |
Correct misassemblies using linked or long reads
|
2025-03-25 |
|
bioconductor-elmer
|
public |
Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes
|
2025-03-25 |
|
bioconductor-elmer.data
|
public |
Data for the ELMER package
|
2025-03-25 |
