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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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2025-04-22 |
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simka
|
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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2025-04-22 |
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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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2025-04-22 |
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topas
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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.
|
2025-04-22 |
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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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2025-04-22 |
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rpf-count-cds
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public |
A python script for counting RPF reads map to CDS region.
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2025-04-22 |
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biopet-bamstats
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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.
|
2025-04-22 |
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scanpy
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public |
Single-Cell Analysis in Python. Scales to >1M cells.
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2025-04-22 |
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comparems2
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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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2025-04-22 |
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abeona
|
public |
A simple transcriptome assembler based on kallisto and Cortex graphs.
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2025-04-22 |
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delegation
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public |
Simple implementation of the delegate pattern.
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2025-04-22 |
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cortexpy
|
public |
A Python API for manipulating (Mc)Cortex de novo assembly graph and link data
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2025-04-22 |
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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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2025-04-22 |
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lightassembler
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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.
|
2025-04-22 |
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mccortex
|
public |
De novo genome assembly and multisample variant calling
|
2025-04-22 |
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thermorawfileparser
|
public |
Wrapper around the .net (C#) ThermoFisher ThermoRawFileReader library for running on Linux with mono
|
2025-04-22 |
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bandage
|
public |
Bandage - a Bioinformatics Application for Navigating De novo Assembly Graphs Easily.
|
2025-04-22 |
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stream
|
public |
STREAM-Single-cell Trajectories Reconstruction, Exploration And Mapping
|
2025-04-22 |
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arb-bio-devel
|
public |
ARB 6 Sequence Analysis Suite
|
2025-04-22 |
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arb-bio-tools
|
public |
ARB 6 Sequence Analysis Suite
|
2025-04-22 |
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libarbdb
|
public |
ARB 6 Sequence Analysis Suite
|
2025-04-22 |
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zerone
|
public |
Zerone discretizes several ChIP-seq replicates simultaneously and resolves conflicts between them.
|
2025-04-22 |
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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.
|
2025-04-22 |
|
gatb
|
public |
The Genome Analysis Toolbox with de-Bruijn graph
|
2025-04-22 |
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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.
|
2025-04-22 |
