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 a collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.

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.

Very fast parallel big-data BLAST XML file parser which can be used as command line utility. Use blastxmlparser to: Parse BLAST XML; filter output; generate FASTA, JSON, YAML, RDF, JSON-LD, HTML, CSV, tabular output etc.

SeuratWrappers is a collection of community-provided methods and extensions for Seurat, curated by the Satija Lab at NYGC. These methods comprise functionality not presently found in Seurat, and are able to be updated much more frequently.

LibSBML is a library to help you read, write, manipulate, translate, and validate SBML files and data streams. The Systems Biology Markup Language (SBML) is an interchange format for computer models of biological processes. SBML is useful for models of metabolism, cell signaling, and more. It continues to be evolved and expanded by an international community.

A tandem repeat in DNA is two or more adjacent, approximate copies of a pattern of nucleotides. Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences. In order to use the program, the user submits a sequence in FASTA format. The output consists of two files: a repeat table file and an alignment file. Submitted sequences may be of arbitrary length. Repeats with pattern size in the range from 1 to 2000 bases are detected.

This package is a Python-based command line interface for processing .bam files with mitochondrial reads and generating high-quality heteroplasmy estimation from sequencing data. The mgatk package places a special emphasis on mitochondrial genotypes generated from single-cell genomics data, primarily mtscATAC-seq, but is generally applicable across other assays.

MAFFT offers a range of multiple alignment methods for nucleotide and protein sequences. For instance, it offers L-INS-i (accurate; for alignment of <~200 sequences) and FFT-NS-2 (fast; for alignment of <~30,000 sequences).

dRep is a Python program for rapidly comparing large numbers of genomes. dRep can also "de-replicate" a genome set by identifying groups of highly similar genomes and choosing the best representative genome for each genome set.

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

scprep provides an all-in-one framework for loading, preprocessing, and plotting matrices in Python, with a focus on single-cell genomics.

This package provides utility functions and imports for Giotto Suite.

This package provides tools for handling BAM, SAM, Tabix, bgzf, CRAM, CSIv1, CSIv2 and FAI files.

Piranha is a peak-caller for genomic data produced by CLIP-seq and RIP-seq experiments. It takes input in BED or BAM format and identifies regions of statistically significant read enrichment. Additional covariates may optionally be provided to further inform the peak-calling process.

This package provides bioinformatic tools to align, deduplicate, reformat, filter and normalize DNA and RNA-seq data. It includes the following tools: BBMap, a short read aligner for DNA and RNA-seq data; BBNorm, a kmer-based error-correction and normalization tool; Dedupe, a tool to simplify assemblies by removing duplicate or contained subsequences that share a target percent identity; Reformat, to convert reads between fasta/fastq/scarf/fasta+qual/sam, interleaved/paired, and ASCII-33/64, at over 500 MB/s; and BBDuk, a tool to filter, trim, or mask reads with kmer matches to an artifact/contaminant file.

This package contains gatingTemplates, example fcs files and compensation controls for use in CytoExploreR.

Picard is a set of Java command line tools for manipulating high-throughput sequencing (HTS) data and formats. Picard is implemented using the HTSJDK Java library to support accessing file formats that are commonly used for high-throughput sequencing data such as SAM, BAM, CRAM and VCF.

Fastp is a tool designed to provide fast all-in-one preprocessing for FastQ files. This tool has multi-threading support to afford high performance.

This package provides a method to detect and enable removal of doublets from single-cell RNA-sequencing.

The package reads phylogenetic data in the phyloXML format. It also includes functions for writing data in this format.

This package contains functions for the SCENT algorithm. SCENT uses single-cell multimodal data and links ATAC-seq peaks to their target genes by modeling association between chromatin accessibility and gene expression across individual single cells.

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

This package provides graphical user interfaces to organize and visualize Nanopore sequencing data.