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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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2025-04-22 |
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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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2025-04-22 |
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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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2025-04-22 |
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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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2025-04-22 |
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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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2025-04-22 |
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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
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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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2025-04-22 |
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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.
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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.
|
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).
|
2025-04-22 |
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abeona
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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
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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
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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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thermorawfileparser
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public |
Wrapper around the .net (C#) ThermoFisher ThermoRawFileReader library for running on Linux with mono
|
2025-04-22 |
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bandage
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public |
Bandage - a Bioinformatics Application for Navigating De novo Assembly Graphs Easily.
|
2025-04-22 |
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stream
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public |
STREAM-Single-cell Trajectories Reconstruction, Exploration And Mapping
|
2025-04-22 |
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arb-bio-devel
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public |
ARB 6 Sequence Analysis Suite
|
2025-04-22 |
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arb-bio-tools
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public |
ARB 6 Sequence Analysis Suite
|
2025-04-22 |
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libarbdb
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public |
ARB 6 Sequence Analysis Suite
|
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 |
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gatb
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public |
The Genome Analysis Toolbox with de-Bruijn graph
|
2025-04-22 |
