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pftools
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public |
A generalized profile syntax for biomolecular sequence motifs and its function in automatic sequence interpretation.
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2025-10-13 |
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cyvcf2
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public |
A cython wrapper around htslib built for fast parsing of Variant Call Format (VCF) files.
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2025-10-13 |
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art_modern
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public |
Modernized ART simulator of diverse Next-Generation Sequencing reads
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2025-10-13 |
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dipper
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public |
DIPPER: An ultrafast tool for phylogenetic tree reconstruction.
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2025-10-13 |
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pbstarphase
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public |
A phase-aware pharmacogenomic diplotyper for PacBio sequencing data
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2025-10-13 |
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grzctl
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public |
Control CLI for GRZ administrators.
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2025-10-13 |
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grz-cli
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public |
Tool for validation, encryption and upload of MV submissions to GDCs.
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2025-10-13 |
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grz-pydantic-models
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public |
Pydantic models for the GRZ metadata schema
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2025-10-13 |
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grz-db
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public |
SQL models for grz-cli and grz-watchdog
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2025-10-13 |
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grz-common
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public |
Common library for grz applications.
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2025-10-13 |
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latch
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public |
The Latch python bioinformatics framework.
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2025-10-12 |
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skani
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public |
skani is a fast and robust tool for calculating ANI between metagenome assembled genomes and contigs.
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2025-10-12 |
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srf-n-trf
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public |
Extract specific monomers, motifs, and regions from srf and trf output
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2025-10-12 |
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gb-io
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public |
A Python interface to gb-io, a fast GenBank parser and serializer written in Rust.
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2025-10-12 |
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pyabpoa
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public |
pyabpoa: SIMD-based partial order alignment using adaptive band
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2025-10-12 |
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abpoa
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public |
abPOA: fast SIMD-based partial order alignment using adaptive band.
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2025-10-12 |
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unifrac
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public |
Fast phylogenetic diversity calculations.
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2025-10-12 |
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r-signac
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public |
A framework for the analysis and exploration of single-cell chromatin data. The 'Signac' package contains functions for quantifying single-cell chromatin data, computing per-cell quality control metrics, dimension reduction and normalization, visualization, and DNA sequence motif analysis.
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2025-10-12 |
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sopa
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public |
Spatial-omics pipeline and analysis.
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2025-10-12 |
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r-structssi
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public |
Performs multiple testing corrections that take specific structure of hypotheses into account.
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2025-10-12 |
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netmd
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public |
NetMD is a computational method for identifying consensus behavior across multiple molecular dynamics simulations.
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2025-10-12 |
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zol
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public |
zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters.
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2025-10-11 |
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foldmason
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public |
Multiple Protein Structure Alignment at Scale with FoldMason
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2025-10-11 |
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r-numbat
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public |
A computational method that infers copy number variations (CNVs) in cancer scRNA-seq data and reconstructs the tumor phylogeny. 'numbat' integrates signals from gene expression, allelic ratio, and population haplotype structures to accurately infer allele-specific CNVs in single cells and reconstruct their lineage relationship. 'numbat' can be used to: 1. detect allele-specific copy number variations from single-cells; 2. differentiate tumor versus normal cells in the tumor microenvironment; 3. infer the clonal architecture and evolutionary history of profiled tumors. 'numbat' does not require tumor/normal-paired DNA or genotype data, but operates solely on the donor scRNA-data data (for example, 10x Cell Ranger output). Additional examples and documentations are available at <https://kharchenkolab.github.io/numbat/>. For details on the method please see Gao et al. Nature Biotechnology (2022) <doi:10.1038/s41587-022-01468-y>.
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2025-10-10 |
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orthanq
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public |
Uncertainty aware HLA typing and general haplotype quantification.
|
2025-10-10 |
