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

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.

PhyML is a software package that uses modern statistical approaches to analyse alignments of nucleotide or amino acid sequences in a phylogenetic framework. The main tool in this package builds phylogenies under the maximum likelihood criterion. It implements a large number of substitution models coupled with efficient options to search the space of phylogenetic tree topologies. codePhyREX fits the spatial-Lambda-Fleming-Viot model to geo-referenced genetic data. This model is similar to the structured coalescent but assumes that individuals are distributed along a spatial continuum rather than discrete demes. PhyREX can be used to estimate population densities and rates of dispersal. Its output can be processed by treeannotator (from the BEAST package) as well as SPREAD.

SAIGE is a package for efficiently controlling for case-control imbalance and sample relatedness in single-variant assoc tests (SAIGE) and controlling for sample relatedness in region-based assoc tests in large cohorts and biobanks (SAIGE-GENE+).

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.

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.

This package provides utility functions for manipulating BAM files.

This tool provides a Python framework to streamline genomics operations. It offers a direct interface to Ensembl genome assemblies and annotations, while also accommodating custom genomes via FASTA/GTF inputs. The primary objective of pybio is to simplify genome management. It achieves this by providing automatic download of Ensembl genome assemblies and annotation, provides Python genomic feature search and sequence retrieval from the managed genomes, STAR indexing and mapping and more.

This library contains the genomics components of the Bio++ sequence library. It is part of the Bio++ project.

NanoSV is a software package that can be used to identify structural genomic variations in long-read sequencing data, such as data produced by Oxford Nanopore Technologies’ MinION, GridION or PromethION instruments, or Pacific Biosciences RSII or Sequel sequencers.

This package provides a VCF parser for Python.

StringTie is a fast and efficient assembler of RNA-Seq sequence alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Its input can include not only the alignments of raw reads used by other transcript assemblers, but also alignments of longer sequences that have been assembled from those reads. To identify differentially expressed genes between experiments, StringTie's output can be processed either by the Cuffdiff or Ballgown programs.

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.

This package is a client implementation of the GA4GH htsget protocol. It provides a simple and reliable way to retrieve genomic data from servers supporting the protocol.

This package provides a fast, JVM-free toolkit for removing duplicate reads from BAM/CRAM. It handles the two major kinds of duplication event in sequencing data, each a faithful, independent port of the standard reference tool, with the performance-critical inner loops accelerated in Cython.

This package is intended to help users to efficiently analyze genomic data resulting from various experiments.

Scanorama enables batch-correction and integration of heterogeneous scRNA-seq datasets, which is described in the paper "Efficient integration of heterogeneous single-cell transcriptomes using Scanorama" by Brian Hie, Bryan Bryson, and Bonnie Berger.

This package is a rasterization preprocessing framework that aggregates cellular information into spatial pixels to reduce resource requirements for spatial omics data analysis. SEraster reduces the number of points in spatial omics datasets for downstream analysis through a process of rasterization where single cells gene expression or cell-type labels are aggregated into equally sized pixels based on a user-defined resolution. SEraster can be incorporated with other packages to conduct downstream analyses for spatial omics datasets, such as detecting spatially variable genes.

PyEGA3 is a tool for viewing and downloading files from authorized EGA datasets. It uses the EGA data API and has several key features:

• Files are transferred over secure https connections and received unencrypted, so no need for decryption after download.

• Downloads resume from where they left off in the event that the connection is interrupted.

• Supports file segmenting and parallelized download of segments, improving overall performance.

• After download completes, file integrity is verified using checksums.

• Implements the GA4GH-compliant htsget protocol for download of genomic ranges for data files with accompanying index files.

VoltRonStore provides utilities and a resource for installing dependencies of VoltRon package.

This package builds on Seurat's Doheatmap function code to produce a heatmap from a Seurat object with multiple annotation bars.

Drop-seq is a technology to enable biologists to analyze RNA expression genome-wide in thousands of individual cells at once. This package provides tools to perform Drop-seq analyses.

This package provides tools for dealing with Unique Molecular Identifiers (UMIs) and Random Molecular Tags (RMTs) in genetic sequences. There are six tools: the extract and whitelist commands are used to prepare a fastq containing UMIs +/- cell barcodes for alignment. The remaining commands, group, dedup, and count/count_tab, are used to identify PCR duplicates using the UMIs and perform different levels of analysis depending on the needs of the user.

The loom file format is an efficient format for very large omics datasets, consisting of a main matrix, optional additional layers, a variable number of row and column annotations. Loom also supports sparse graphs. This library makes it easy to work with .loom files for single-cell RNA-seq data.