This is a package providing efficient operations for single cell ATAC-seq fragments and RNA counts matrices. It is interoperable with standard file formats, and introduces efficient bit-packed formats that allow large storage savings and increased read speeds.

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.

CD-HIT is a program for clustering and comparing protein or nucleotide sequences. CD-HIT is designed to be fast and handle extremely large databases.

This program compares version strings. It intends to be a replacement for strverscmp.

The khmer software is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes and single cells. Khmer can make de novo assemblies faster, and sometimes better. Khmer can also identify and fix problems with shotgun data.

Entrez Direct (EDirect) is a method for accessing the National Center for Biotechnology Information's (NCBI) set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a terminal. Functions take search terms from command-line arguments. Individual operations are combined to build multi-step queries. Record retrieval and formatting normally complete the process.

EDirect also provides an argument-driven function that simplifies the extraction of data from document summaries or other results that are returned in structured XML format. This can eliminate the need for writing custom software to answer ad hoc questions.

This package stores motif collections as lists of position frequency matrix (PWMatrixList) objects provided by the TFBSTools package for use in R with packages like motifmatchr or chromVAR.

PAIRADISE is a method for detecting allele-specific alternative splicing (ASAS) from RNA-seq data. Unlike conventional approaches that detect ASAS events one sample at a time, PAIRADISE aggregates ASAS signals across multiple individuals in a population. By treating the two alleles of an individual as paired, and multiple individuals sharing a heterozygous SNP as replicates, PAIRADISE formulates ASAS detection as a statistical problem for identifying differential alternative splicing from RNA-seq data with paired replicates.

This package implements bindings for h5 files that are compatible with Bioconductor S4 data structures, namely the DataFrame and DelayedArray. This allows HDF5-backed data to be easily used as data frames with arbitrary sets of columns.

MyGene.Info provides simple-to-use REST web services to query/retrieve gene annotation data. It's designed with simplicity and performance emphasized. Mygene is a Python wrapper to access MyGene.Info services.

MultiVelo uses a probabilistic latent variable model to estimate the switch time and rate parameters of gene regulation, providing a quantitative summary of the temporal relationship between epigenomic and transcriptomic changes.

Harmony is an algorithm for integrating multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.

This package provides a GFF/GTF file parsing utility providing format conversions, region filtering, FASTA sequence extraction and more.

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

Biopython is a set of tools for biological computation including parsers for bioinformatics files into Python data structures; interfaces to common bioinformatics programs; a standard sequence class and tools for performing common operations on them; code to perform data classification; code for dealing with alignments; code making it easy to split up parallelizable tasks into separate processes; and more.

Bioparser is a C++ header only parsing library for several bioinformatics formats (FASTA/Q, MHAP/PAF/SAM), with support for zlib compressed files.

SEEK is a computational gene co-expression search engine. SEEK provides biologists with a way to navigate the massive human expression compendium that now contains thousands of expression datasets. SEEK returns a robust ranking of co-expressed genes in the biological area of interest defined by the user's query genes. It also prioritizes thousands of expression datasets according to the user's query of interest.

The goal of bedtorch is to provide a fast BED file manipulation tool suite native in R.

The gdc-client provides several convenience functions over the GDC API which provides general download/upload via HTTPS.

VoltRon is a novel spatial omic analysis toolbox for multi-omics integration using spatial image registration. VoltRon is capable of analyzing multiple types and modalities of spatially-aware datasets. VoltRon visualizes and analyzes regions of interests (ROIs), spots, cells and even molecules.

The phylo module provides a biojava interface layer to the forester phylogenomics library for constructing phylogenetic trees.

CGAT-core is a set of libraries and helper functions used to enable researchers to design and build computational workflows for the analysis of large-scale data-analysis.

This is a set of R functions that allows you to generate precise figures. This tool will create clean markdown reports about what you just discovered.

Chromap is a fast method for aligning and preprocessing high throughput chromatin profiles. Typical use cases include:

• trimming sequencing adapters, mapping bulk ATAC-seq or ChIP-seq genomic reads to the human genome and removing duplicates;

• trimming sequencing adapters, mapping single cell ATAC-seq genomic reads to the human genome, correcting barcodes, removing duplicates and performing Tn5 shift;

• split alignment of Hi-C reads against a reference genome.