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auspice
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public |
Auspice is an open-source interactive tool for visualising phylogenomic data
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2025-09-06 |
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methbat
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public |
A battery of methylation tools for PacBio HiFi reads
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2025-09-05 |
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mageck
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public |
MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout), an algorithm to process, QC, analyze and visualize CRISPR screening data.
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2025-09-05 |
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pqlseqpy
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public |
Fast PQLseq in Python
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2025-09-05 |
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bird_tool_utils_python
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public |
Python utilities used as part of the bird suite of bioinformatic tools.
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2025-09-05 |
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cascade-reg
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public |
Causal discovery of gene regulatory programs from single-cell genomics
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2025-09-05 |
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afpdb
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public |
A Numpy-based PDB structure manipulation package
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2025-09-05 |
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gsalign
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public |
GSAlign: an ultra-fast sequence alignment tool
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2025-09-05 |
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scalpel
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public |
Sensitive detection of INDELs (INsertions and DELetions)
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2025-09-04 |
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galah
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public |
Galah aims to be a more scalable metagenome assembled genome (MAG) dereplication method.
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2025-09-04 |
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variant_tools
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public |
Integrated annotation and analysis of next gen sequencing data
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2025-09-04 |
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hgvs
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public |
HGVS Parser, Formatter, Mapper, and Validator.
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2025-09-04 |
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peregrine-2021
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public |
A genome assembler designed for long-reads that have good enough accuracy
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2025-09-04 |
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primalbedtools
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public |
A collection of tools for working with primer.bed files.
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2025-09-04 |
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iseq
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public |
iSeq is a Bash script that allows you to download sequencing data and metadata from GSA, SRA, ENA, and DDBJ databases.
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2025-09-04 |
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mess
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public |
Snakemake pipeline for simulating shotgun metagenomic samples
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2025-09-04 |
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peptides
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public |
Physicochemical properties, indices and descriptors for amino-acid sequences.
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2025-09-04 |
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hostile
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public |
Hostile: accurate host decontamination.
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2025-09-04 |
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r-dartr
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public |
Functions are provided that facilitate the import and analysis of SNP (single nucleotide polymorphism) and silicodart (presence/absence) data. The main focus is on data generated by DarT (Diversity Arrays Technology). However, once SNP or related fragment presence/absence data from any source is imported into a genlight object many of the functions can be used. Functions are available for input and output of SNP and silicodart data, for reporting on and filtering on various criteria (e.g. CallRate, Heterozygosity, Reproducibility, maximum allele frequency). Advanced filtering is based on Linkage Disequilibrium and HWE (Hardy-Weinberg equilibrium). Other functions are available for visualization after PCoA (Principle Coordinate Analysis), or to facilitate transfer of data between genlight/genind objects and newhybrids, related, phylip, structure, faststructure packages.
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2025-09-04 |
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flexsweep
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public |
A versatile tool for detecting selective sweeps.
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2025-09-04 |
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r-dinamic.duo
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public |
In tumor tissue, underlying genomic instability can lead to DNA copy number alterations, e.g., copy number gains or losses. Sporadic copy number alterations occur randomly throughout the genome, whereas recurrent alterations are observed in the same genomic region across multiple independent samples, perhaps because they provide a selective growth advantage. Here we use cyclic shift permutations to identify recurrent copy number alterations in a single cohort or recurrent copy number differences in two cohorts based on a common set of genomic markers. Additional functionality is provided to perform downstream analyses, including the creation of summary files and graphics. DiNAMIC.Duo builds upon the original DiNAMIC package of Walter et al. (2011) <doi:10.1093/bioinformatics/btq717> and leverages the theory developed in Walter et al. (2015) <doi:10.1093/biomet/asv046>. A manuscript based on DiNAMIC.Duo is currently under development.
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2025-09-04 |
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phame
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public |
A tool to derive SNP matrices and phylogenetic tree from raw reads, contigs, and full genomes.
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2025-09-04 |
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jalview
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public |
Jalview is a free program for multiple sequence alignment editing, visualisation, analysis and figure generation.
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2025-09-04 |
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genome2tree
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public |
A pipeline to build phylogenetic trees from genome comparisons
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2025-09-04 |
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rseqc
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public |
QC package for RNA-seq data.
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2025-09-04 |
