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

Sailfish is a tool for genomic transcript quantification from RNA-seq data. It requires a set of target transcripts (either from a reference or de-novo assembly) to quantify. All you need to run sailfish is a fasta file containing your reference transcripts and a (set of) fasta/fastq file(s) containing your reads.

This package implements parallel block gzip. For many formats, in particular genomics data formats, data are compressed in fixed-length blocks such that they can be easily indexed based on a (genomic) coordinate order, since typically each block is sorted according to this order. This allows for each block to be individually compressed (deflated), or more importantly, decompressed (inflated), with the latter enabling random retrieval of data in large files (gigabytes to terabytes). pbgzip is not limited to any particular format, but certain features are tailored to genomics data formats when enabled. Parallel decompression is somewhat faster, but the true speedup comes during compression.

This package aims to simplify working with genomic region / interval data by providing a common interface that lets you access a wide selection of file types and formats for handling genomic region data---all using the same syntax.

Scallop is a reference-based transcript assembler. Scallop features its high accuracy in assembling multi-exon transcripts as well as lowly expressed transcripts.

SQUID is Sean Eddy's personal library of C functions and utility programs for sequence analysis.

This package provides procedures for efficient pythonic random access to fasta subsequences.

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.

Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data. It was developed for the use in a clinical research setting. Therefore, short runtimes and high sensitivity were important design criteria. It is based on the fast STAR aligner and the post-alignment runtime is typically just around two minutes. In contrast to many other fusion detection tools which build on STAR, Arriba does not require to reduce the alignIntronMax parameter of STAR to detect small deletions.

CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.

Bio-locus is a tabix-like tool for fast querying of genome locations. Many file formats in bioinformatics contain records that start with a chromosome name and a position for a SNP, or a start-end position for indels. Bio-locus allows users to store this chr+pos or chr+pos+alt information in a database.

eXpress is a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences. Example applications include transcript-level RNA-Seq quantification, allele-specific/haplotype expression analysis (from RNA-Seq), transcription factor binding quantification in ChIP-Seq, and analysis of metagenomic data.

PhenoGraph is a clustering method designed for high-dimensional single-cell data. It works by creating a graph representing phenotypic similarities between cells and then identifying communities in this graph.

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

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.

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.

Hotspot is a tool for identifying informative genes (and gene modules) in a single-cell dataset. Importantly, "informative" is decided based on how well a gene's variation agrees with some cell metric---some similarity mapping between cells. Genes which are informative are those whose expression varies in similar way among cells which are nearby in the given metric.

dnaio is a Python library for fast parsing of FASTQ and also FASTA files. The code was previously part of the cutadapt tool.

Change-O is a collection of tools for processing the output of V(D)J alignment tools, assigning clonal clusters to immunoglobulin (Ig) sequences, and reconstructing germline sequences.

This package provides a VCF parser for Python.

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.

CodeAndRoll2 is a set of more than 130 productivity functions. These functions are used by MarkdownReports, ggExpress, and SeuratUtils.

This R package lets you estimate signatures of mutational processes and their activities on mutation count data. Starting from a set of single-nucleotide variants (SNVs), it allows both estimation of the exposure of samples to predefined mutational signatures (including whether the signatures are present at all), and identification of signatures de novo from the mutation counts.

This package provides a method to sample cells from single-cell data. It also generates an aggregate profile on a pruned K-Nearest Neighbor graph. This approach leads to an improved gene expression profile for quantifying gene regulations.