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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 |
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biobb_io
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public |
Biobb_io is the Biobb module collection to fetch data to be consumed by the rest of the Biobb building blocks.
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2025-09-04 |
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biobb_pdb_tools
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public |
Biobb_pdb_tools is a swiss army knife for manipulating and editing PDB files.
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2025-09-04 |
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dms
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public |
Comprehensive taxonomic and phylogenetic comparison of shotgun metagenomes at the species level
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2025-09-04 |
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fairease-source
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public |
SOURCE: Sea Observations Utility for Reprocessing, Calibration and Evaluation.
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2025-09-04 |
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pyrle
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public |
Genomic Rle-objects for Python
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2025-09-04 |
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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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2025-09-04 |
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goleft
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public |
goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary
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2025-09-04 |
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gridss
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public |
GRIDSS: the Genomic Rearrangement IDentification Software Suite
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2025-09-04 |
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grabix
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public |
a wee tool for random access into BGZF files.
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2025-09-04 |
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umis
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public |
Tools for processing UMI RNA-tag data
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2025-09-04 |
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atropos
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public |
trim adapters from high-throughput sequencing reads
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2025-09-04 |
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hmmcopy
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public |
C++ based programs for analyzing BAM files and preparing read counts -- used with bioconductor-hmmcopy
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2025-09-04 |
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mawk
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public |
mawk is an interpreter for the AWK Programming Language.
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2025-09-04 |
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pod5
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public |
Oxford Nanopore Technologies Pod5 File Format Python API and Tools.
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2025-09-04 |
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decenttree
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public |
Scalable Neighbour-Joining and related algorithms for phylogenetic inference
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2025-09-04 |
