The SRA Toolkit from NCBI is a collection of tools and libraries for reading of sequencing files from the Sequence Read Archive (SRA) database and writing files into the .sra format.

Express Beta Diversity (EBD) calculates ecological beta diversity (dissimilarity) measures between biological communities. EBD implements a variety of diversity measures including those that make use of phylogenetic similarity of community members.

This package provides a collection of methods to extract gene programs from single-cell gene expression data using non-negative matrix factorization (NMF). GeneNMF contains functions to directly interact with the Seurat toolkit and derive interpretable gene program signatures.

python-cwl-upgrader is a standalone upgrader for CWL documents from version draft-3, v1.0, and v1.1 to v1.2.

MAGIC is an interactive tool to impute missing values in single-cell sequencing data and to restore the structure of the data. It also provides data pre-processing functionality such as dimensionality reduction and gene expression visualization.

PDBFixer is designed to rectify issues in Protein Data Bank files. Its intuitive interface simplifies the process of resolving problems encountered in PDB files prior to simulation tasks.

Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF.

This is an R package providing additional capabilities and speed for GenomicRanges operations.

This package provides data for the SeuratExtend tool.

This package is a set of R functions for generating precise figures. This tool helps you to create clean markdown reports about what you just discovered with your analysis script.

This is a package that lets you process UMI-4C data from scratch to produce nice plots.

This is an R package for pre-processing of flow and mass cytometry data. This package includes panel editing or renaming for FCS files, bead-based normalization and debarcoding.

This tool is for building Generalized Additive Models in Python. It emphasizes modularity and performance. The API will be immediately familiar to anyone with experience of scikit-learn or scipy.

This package lets you read and write the PLINK BED format, simply and efficiently.

Sleuth is a program for differential analysis of RNA-Seq data. It makes use of quantification uncertainty estimates obtained via Kallisto for accurate differential analysis of isoforms or genes, allows testing in the context of experiments with complex designs, and supports interactive exploratory data analysis via sleuth live.

This is a package for fast Non-negative Matrix Factorization (NMF) with automatic rank-determination for dimension reduction of single-cell data using Seurat, RcppML nmf, SingleCellExperiments and similar.

Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. This library provides sequence-related modules.

This is an R package to build generic .loom files aligning with the default naming convention of the .loom format and to integrate other data types e.g.: regulons (SCENIC), clusters from Seurat, trajectory information... The package can also be used to extract data from .loom files.

This package provides Python bindings for spoa, a C++ implementation of the partial order alignment (POA) algorithm (as described in 10.1093/bioinformatics/18.3.452) which is used to generate consensus sequences

Savvy is the official C++ interface for the SAV file format and offers seamless support for BCF and VCF files.

This package offers a set of functions to use in order to compute communities on graphs weighted or unweighted.

This package performs a fast Wilcoxon rank sum test and auROC analysis.

Pando leverages multi-modal single-cell measurements to infer gene regulatory networks using a flexible linear model-based framework. By modeling the relationship between TF-binding site pairs with the expression of target genes, Pando simultaneously infers gene modules and sets of regulatory regions for each transcription factor.

FAN-C provides a pipeline for analysing Hi-C data starting at mapped paired-end sequencing reads.