Bioinformaticians often have to convert sequence files between formats and do little manipulations on them, and it's not worth writing scripts for that. Seqmagick is a utility to expose the file format conversion in BioPython in a convenient way. Instead of having a big mess of scripts, there is one that takes arguments.

BioJava is a project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats, reference implementations of popular algorithms, and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics.

This package provides the core libraries.

HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). In addition to using one global graph FM (GFM) index that represents a population of human genomes, HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome. These small indexes, combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. This new indexing scheme is called a Hierarchical Graph FM index (HGFM).

This is package for including transposable elements in differential enrichment analysis of sequencing datasets. TEtranscripts and TEcount take RNA-seq (and similar data) and annotates reads to both genes and transposable elements. TEtranscripts then performs differential analysis using DESeq2. Note that TEtranscripts and TEcount rely on specially curated GTF files, which are not included due to their size.

bx-python provides tools for manipulating biological data, particularly multiple sequence alignments.

This package implements methods for batch correction and integration of scRNA-seq datasets, based on the Seurat anchor-based integration framework. In particular, STACAS is optimized for the integration of heterogeneous datasets with only limited overlap between cell sub-types (e.g. TIL sets of CD8 from tumor with CD8/CD4 T cells from lymphnode), for which the default Seurat alignment methods would tend to over-correct biological differences. The 2.0 version of the package allows the users to incorporate explicit information about cell-types in order to assist the integration process.

This package provides R miscellaneous utilities for basic data manipulation, debugging, visualization, lsf management, and common mskilab tasks.

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 computational toolkit in R for the integration, exploration, and analysis of high-dimensional single-cell cytometry and imaging data.

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.

BLAST is a popular method of performing a DNA or protein sequence similarity search, using heuristics to produce results quickly. It also calculates an “expect value” that estimates how many matches would have occurred at a given score by chance, which can aid a user in judging how much confidence to have in an alignment.

This package implements the method csSAM that computes cell-specific differential expression from measured cell proportions using SAM.

The porechop package is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads. Porechop performs thorough alignments to effectively find adapters, even at low sequence identity. Porechop also supports demultiplexing of Nanopore reads that were barcoded with the Native Barcoding Kit, PCR Barcoding Kit or Rapid Barcoding Kit.

PiGx SARS-CoV-2 is a pipeline for analysing data from sequenced wastewater samples and identifying given variants-of-concern of SARS-CoV-2. The pipeline can be used for continuous sampling. The output report will provide an intuitive visual overview about the development of variant abundance over time and location.

ReadWriter is a set of R functions to read and write files conveniently.

HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).

Segemehl is software to map short sequencer reads to reference genomes. Segemehl implements a matching strategy based on enhanced suffix arrays (ESA). It accepts fasta and fastq queries (gzip'ed and bgzip'ed). In addition to the alignment of reads from standard DNA- and RNA-seq protocols, it also allows the mapping of bisulfite converted reads (Lister and Cokus) and implements a split read mapping strategy. The output of segemehl is a SAM or BAM formatted alignment file.

Grassroots DICOM (GDCM) is an implementation of the DICOM standard designed to be open source so that researchers may access clinical data directly. GDCM includes a file format definition and a network communications protocol, both of which should be extended to provide a full set of tools for a researcher or small medical imaging vendor to interface with an existing medical database.

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

RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. The RSEM package provides a user-friendly interface, supports threads for parallel computation of the EM algorithm, single-end and paired-end read data, quality scores, variable-length reads and RSPD estimation. In addition, it provides posterior mean and 95% credibility interval estimates for expression levels. For visualization, it can generate BAM and Wiggle files in both transcript-coordinate and genomic-coordinate.

This package aims to bring the power and flexibility of AnnData to the R ecosystem, allowing you to effortlessly manipulate and analyze your single-cell data. This package lets you work with backed h5ad and zarr files, directly access various slots (e.g. X, obs, var), or convert the data into SingleCellExperiment and Seurat objects.

CoolBox is a toolkit for visual analysis of genomics data. It aims to be highly compatible with the Python ecosystem, easy to use and highly customizable with a well-designed user interface. It can be used in various visualization situations, for example, to produce high-quality genome track plots or fetch common used genomic data files with a Python script or command line, interactively explore genomic data within Jupyter environment or web browser.

genomepy is designed to provide a simple and straightforward way to download and use genomic data. This includes

1. searching available data,

2. showing the available metadata,

3. automatically downloading, preprocessing and matching data, and

4. generating optional aligner indexes.

All with sensible, yet controllable defaults.

Phylogenetic Analysis with Space/Time models (PHAST) is a collection of command-line programs and supporting libraries for comparative and evolutionary genomics. Best known as the search engine behind the Conservation tracks in the University of California, Santa Cruz (UCSC) Genome Browser, PHAST also includes several tools for phylogenetic modeling, functional element identification, as well as utilities for manipulating alignments, trees and genomic annotations.