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kraken2
|
public |
Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.
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2025-02-18 |
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gappa
|
public |
Genesis Applications for Phylogenetic Placement Analysis
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2025-02-18 |
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clipkit
|
public |
Alignment trimming software for phylogenetics.
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2025-02-18 |
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gencove
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public |
Gencove is a high-throughput, cost-effective platform for genome sequencing and analysis. This command-line interface can be used to easily access the Gencove API.
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2025-02-18 |
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icescreen
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public |
ICEscreen detects and annotates ICEs (Integrative and Conjugative Elements) and IMEs (Integrative and Mobilizable Elements) in Bacillota genomes.
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2025-02-18 |
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gw
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public |
View genomic sequencing data and vcf files
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2025-02-18 |
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ensembl-utils
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public |
Ensembl Python general-purpose utils
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2025-02-18 |
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r-stitch
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public |
STITCH - Sequencing To Imputation Through Constructing Haplotypes.
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2025-02-18 |
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perl-error
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public |
Error/exception handling in an OO-ish way
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2025-02-18 |
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hmftools-chord
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public |
Predict HRD using somatic mutations contexts
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2025-02-18 |
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hmftools-sage
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public |
SAGE is a somatic SNV, MNV and small INDEL caller optimised 100x tumor / 40x normal coverage, but has a flexible set of filters that can be adapted to lower or higher depth coverage.
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2025-02-18 |
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hmftools-purple
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public |
PURPLE is a purity ploidy estimator for tumor samples.
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2025-02-18 |
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mutalyzer_hgvs_parser
|
public |
Mutalyzer HGVS variant description parser
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2025-02-18 |
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met4j
|
public |
Met4J is an open-source Java library dedicated to the structural analysis of metabolic networks
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2025-02-17 |
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genin2
|
public |
Genin2 is a lightining-fast bioinformatic tool to predict genotypes for H5 viruses belonging to the European clade 2.3.4.4b
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2025-02-17 |
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souporcell
|
public |
Clustering scRNAseq by genotypes.
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2025-02-17 |
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skder
|
public |
skDER & CiDDER: efficient & high-resolution dereplication methods for microbial genomes
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2025-02-17 |
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fastahack
|
public |
No Summary
|
2025-02-17 |
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wgatools
|
public |
A Rust library and tools for whole genome alignment files.
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2025-02-17 |
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metafx
|
public |
MetaFX (METAgenomic Feature eXtraction) is a library for feature extraction from whole-genome metagenome sequencing data and classification of groups of samples.
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2025-02-17 |
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bionumpy
|
public |
Library for working with biological sequence data as numpy arrays.
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2025-02-17 |
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marti
|
public |
Metagenomic Analysis in Real Time
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2025-02-17 |
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r-pathfindr
|
public |
Enrichment analysis enables researchers to uncover mechanisms underlying a phenotype. However, conventional methods for enrichment analysis do not take into account protein-protein interaction information, resulting in incomplete conclusions. pathfindR is a tool for enrichment analysis utilizing active subnetworks. The main function identifies active subnetworks in a protein-protein interaction network using a user-provided list of genes and associated p values. It then performs enrichment analyses on the identified subnetworks, identifying enriched terms (i.e. pathways or, more broadly, gene sets) that possibly underlie the phenotype of interest. pathfindR also offers functionalities to cluster the enriched terms and identify representative terms in each cluster, to score the enriched terms per sample and to visualize analysis results. The enrichment, clustering and other methods implemented in pathfindR are described in detail in Ulgen E, Ozisik O, Sezerman OU. 2019. pathfindR: An R Package for Comprehensive Identification of Enriched Pathways in Omics Data Through Active Subnetworks. Front. Genet. <doi:10.3389/fgene.2019.00858>.
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2025-02-17 |
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svaba
|
public |
Structural variation and indel detection by local assembly
|
2025-02-17 |
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neffy
|
public |
A Python interface of NEFFy C++ tool: NEFF Calculator and MSA File Converter
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2025-02-17 |
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predictosaurus
|
public |
Predictosaurus is a command-line tool designed for uncertainty-aware haplotype-based genomic variant effect prediction.
|
2025-02-17 |
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circtools
|
public |
circtools - a circular RNA toolbox.
|
2025-02-17 |
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seg-suite
|
public |
The seg suite provides tools for manipulating segments, alignments, and annotations of sequences.
|
2025-02-17 |
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hmftools-cobalt
|
public |
Calculate read-depth counts and GC ratios to use in PURPLE.
|
2025-02-17 |
|
hmftools-amber
|
public |
Generates a tumor BAF file for use in PURPLE.
|
2025-02-17 |
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hmftools-bam-tools
|
public |
Rapidly process BAMs for various tasks.
|
2025-02-17 |
|
sdrf-pipelines
|
public |
Translate, convert SDRF to configuration pipelines
|
2025-02-16 |
|
truvari
|
public |
Structural variant comparison tool for VCFs
|
2025-02-16 |
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fastoma
|
public |
FastOMA - a package to infer orthology information among proteomes
|
2025-02-16 |
|
sevenbridges-python
|
public |
SBG API python client bindings
|
2025-02-16 |
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pronto
|
public |
Python frontend to ontologies.
|
2025-02-16 |
|
pbsim3
|
public |
A simulator for all types of Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) long reads
|
2025-02-15 |
|
tir-learner
|
public |
An ensemble pipeline for terminal inverted repeat (TIR) transposable elements annotation.
|
2025-02-15 |
|
hitac
|
public |
A hierarchical taxonomic classifier for fungal ITS sequences
|
2025-02-15 |
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snakemake-executor-plugin-slurm-jobstep
|
public |
A Snakemake executor plugin for running srun jobs inside of SLURM jobs (meant for internal use by snakemake-executor-plugin-slurm)
|
2025-02-15 |
|
metabolights-utils
|
public |
MetaboLights open metabolomics data repository command line interface (CLI), common MetaboLights data models, utility methods and classes.
|
2025-02-15 |
|
vitap
|
public |
Viral Taxonomic Assignment Pipeline
|
2025-02-15 |
|
chopper
|
public |
A rust command line for filtering and trimming long reads.
|
2025-02-15 |
|
r-metacoder
|
public |
A set of tools for parsing, manipulating, and graphing data classified by a hierarchy (e.g. a taxonomy).
|
2025-02-14 |
|
ucsc-cell-browser
|
public |
A browser for single-cell data, main site at http://cells.ucsc.edu. UCSC Cellbrowser, an interactive browser for single cell data. Includes importers and basic pipelines for text files, Seurat, Scanpy and Cellranger. All Javascript - does not require a server backend.
|
2025-02-14 |
|
macs2
|
public |
Model Based Analysis for ChIP-Seq data
|
2025-02-14 |
|
t-coffee
|
public |
A collection of tools for Multiple Alignments of DNA, RNA, Protein Sequence
|
2025-02-14 |
|
pathogen-profiler
|
public |
Library giving access to classes and functions to create a profiling tool to look for mutations from NGS data.
|
2025-02-14 |
|
sainsc
|
public |
Segmentation-free Analysis of In Situ Capture data.
|
2025-02-14 |
|
fastobo
|
public |
Faultless AST for Open Biomedical Ontologies in Python
|
2025-02-14 |
