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bioconductor-sc3-scripts
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public |
A set of wrappers for individual components of the SC3 package. Functions 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.
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2025-04-22 |
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admixture
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public |
ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets.
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2025-04-22 |
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revtrans
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public |
revtrans - performs a reverse translation of a peptide alignment.
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2025-04-22 |
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slimm
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public |
SLIMM - Species Level Identification of Microbes from Metagenomes
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2025-04-22 |
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perl-bundle-bioperl
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public |
A bundle to install external CPAN modules used by BioPerl 1.5.2
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2025-04-22 |
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bpp-popgen
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public |
Bio++ is a set of C++ libraries for Bioinformatics.
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2025-04-22 |
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red
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public |
Red (RepeatsDetector): an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale.
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2025-04-22 |
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truvari
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public |
Structural variant comparison tool for VCFs.
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2025-04-22 |
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gatktool
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public |
Functions and classes used to extend a GATK tool with Python
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2025-04-22 |
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metaxa
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public |
Improved Identification and Taxonomic Classification of Small and Large Subunit rRNA in Metagenomic Data.
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2025-04-22 |
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r-metstat
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public |
A diverse collection of metabolomics related statistical tools.
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2025-04-22 |
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r-popgenome
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public |
Provides efficient tools for population genomics data analysis, able to process individual loci, large sets of loci, or whole genomes. PopGenome <DOI:10.1093/molbev/msu136> not only implements a wide range of population genetics statistics, but also facilitates the easy implementation of new algorithms by other researchers. PopGenome is optimized for speed via the seamless integration of C code.
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2025-04-22 |
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r-blockfest
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public |
An R implementation of an extension of the 'BayeScan' software (Foll, 2008) <DOI:10.1534/genetics.108.092221> for codominant markers, adding the option to group individual SNPs into pre-defined blocks. A typical application of this new approach is the identification of genomic regions, genes, or gene sets containing one or more SNPs that evolved under directional selection.
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2025-04-22 |
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biolib
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public |
Package for common tasks in bioinformatics.
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2025-04-22 |
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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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2025-04-22 |
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cgatcore
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public |
CGAT : the Computational Genomics Analysis Toolkit
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2025-04-22 |
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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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2025-04-22 |
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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 |
