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var-agg
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public |
A simple helper for aggregating multi-sample VCF files into "site VCF" files.
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2025-04-22 |
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rvtests
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public |
Rare variant test software for next generation sequencing data
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2025-04-22 |
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r-epic
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public |
Estimate the Proportion of Immune and Cancer cells from bulk gene expression data.
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2025-04-22 |
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pysradb
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public |
Python package for retrieving metadata and downloading datasets from SRA/ENA/GEO
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2025-04-22 |
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clinvar-tsv
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public |
A Snakemake-based program to download ClinVar and convert to easy-to-use TSV files.
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2025-04-22 |
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svim
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public |
SVIM is a structural variant caller for long reads.
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2025-04-22 |
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bioconductor-dropletutils
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public |
Utilities for Handling Single-Cell Droplet Data
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2025-04-22 |
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pyaavf
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public |
An amino acid variant format parser for Python.
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2025-04-22 |
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r-leapp
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public |
These functions take a gene expression value matrix, a primary covariate vector, an additional known covariates matrix. A two stage analysis is applied to counter the effects of latent variables on the rankings of hypotheses. The estimation and adjustment of latent effects are proposed by Sun, Zhang and Owen (2011). "leapp" is developed in the context of microarray experiments, but may be used as a general tool for high throughput data sets where dependence may be involved.
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2025-04-22 |
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ucsc-cell-browser
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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.
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2025-04-22 |
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metaquantome
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public |
Quantitative metaproteomics analysis of taxonomy and function.
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2025-04-22 |
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r-mcpcounter
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public |
Estimating tissue-infiltrating immune and other stromal subpopulations abundances using gene expression
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2025-04-22 |
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medpy
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public |
Medical image processing in Python
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2025-04-22 |
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libstatgen
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public |
Useful set of classes for creating statistical genetic programs.
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2025-04-22 |
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bgreat
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public |
BGREAT2 is a read mapping tool for NGS sequencing data that align reads on a de Bruijn graph. Preliminary version described at https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1103-9 and used in Bcool a short read corrector (https://arxiv.org/abs/1711.03336)
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2025-04-22 |
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iced
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public |
The python module iced implements the ICE normalization of hic data.
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2025-04-22 |
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btrim
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public |
This tool is made to remove "tips" (short dead ends) from a compacted de Bruijn graph and more generally to remove sequencing errors. Used in Bcool a short read corrector (https://arxiv.org/abs/1711.03336)
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2025-04-22 |
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bioexcel_seqqc
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public |
Sequence Quality Control pipeline/modules
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2025-04-22 |
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r-ebimetagenomics
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public |
Functions for querying the EBI Metagenomics Portal <https://www.ebi.ac.uk/metagenomics/>. The current main focus is on taxa abundance data, but the intention is that this package should evolve into a general purpose package for working with EBI Metagenomics data using R.
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2025-04-22 |
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r-sads
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public |
Maximum likelihood tools to fit and compare models of species abundance distributions and of species rank-abundance distributions.
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2025-04-22 |
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r-breakaway
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public |
Understanding the drivers of microbial diversity is an important frontier of microbial ecology, and investigating the diversity of samples from microbial ecosystems is a common step in any microbiome analysis. 'breakaway' is the premier package for statistical analysis of microbial diversity. 'breakaway' implements the latest and greatest estimates of species richness, as well as the most commonly used estimates. Methods uniquely available in this package include objective Bayes estimators described in Barger and Bunge (2010) <doi:10.1214/10-BA527>, frequency-ratio-based estimators described in Willis and Bunge (2015) <doi:10.1111/biom.12332>, and as described in Willis, Whitman, and Bunge (2016) <doi:10.1111/rssc.12206>, a linear modeling approach for detecting changes in diversity.
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2025-04-22 |
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mhcflurry
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public |
MHC Binding Predictor
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2025-04-22 |
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mhcnames
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public |
Python library for MHC nomenclature parsing
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2025-04-22 |
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metawrap
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public |
MetaWRAP is a pipeline for genome-resolved metagenomic data analysis
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2025-04-22 |
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r-guilds
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public |
A collection of sampling formulas for the unified neutral model of biogeography and biodiversity. Alongside the sampling formulas, it includes methods to perform maximum likelihood optimization of the sampling formulas, methods to generate data given the neutral model, and methods to estimate the expected species abundance distribution. Sampling formulas included in the GUILDS package are the Etienne Sampling Formula (Etienne 2005), the guild sampling formula, where guilds are assumed to differ in dispersal ability (Janzen et al. 2015), and the guilds sampling formula conditioned on guild size (Janzen et al. 2015).
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2025-04-22 |
