This library implements a FASTA and a FASTQ parser without relying on a complex dependency tree.

The preseq package is aimed at predicting and estimating the complexity of a genomic sequencing library, equivalent to predicting and estimating the number of redundant reads from a given sequencing depth and how many will be expected from additional sequencing using an initial sequencing experiment. The estimates can then be used to examine the utility of further sequencing, optimize the sequencing depth, or to screen multiple libraries to avoid low complexity samples.

This package provides Python bindings to the libBigWig library for accessing bigWig files.

This is a drop-in replacement for the IlluminaHumanMethylationEPIC package. It utilizes a Manifest based on 1.0B5 annotation. As of version 0.3.0, the IlluminaHumanMethylationEPIC package still employs the 1.0B2 annotation manifest. A corresponding annotation package, IlluminaHumanMethylationEPICanno.ilm10b5.hg38, is available to ensure proper annotation. The decision to maintain the same name is due to complications in downstream processing caused by array name lookup in certain preprocessing options.

CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.

This package provides a converter between .hic files (from juicer) and single-resolution or multi-resolution .cool files (for cooler). Both hic and cool files describe Hi-C contact matrices.

WhatsHap is software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. It is especially suitable for long reads, but works also well with short reads.

Exonerate is a generic tool for pairwise sequence comparison. It allows the alignment of sequences using a many alignment models, either exhaustive dynamic programming or a variety of heuristics.

This package provides helper functions to detect cross-hybridization on Illumina DNAm arrays.

This package provides Shiny apps for interactive exploration of single-cell data.

Taxtastic is software written in python used to build and maintain reference packages i.e. collections of reference trees, reference alignments, profiles, and associated taxonomic information.

Bamnostic is a pure Python Binary Alignment Map (BAM) file parser and random access tool.

Mudata is a Python package for multi-omics data analysis. It is designed to provide functionality to load, process, and store multimodal omics data.

This package implements the custom CRAM codecs used for "EXTERNAL" block types. These consist of two variants of the rANS codec (8-bit and 16-bit renormalisation, with run-length encoding and bit-packing also supported in the latter), a dynamic arithmetic coder, and custom codecs for name/ID compression and quality score compression derived from fqzcomp.

Straw is library which allows rapid streaming of contact data from .hic files. This package provides Python bindings.

The IDR (Irreproducible Discovery Rate) framework is a unified approach to measure the reproducibility of findings identified from replicate experiments and provide highly stable thresholds based on reproducibility.

muon is a multimodal omics Python framework.

This package provides an RNA-seq workflow for differential transcript usage (DTU) following Salmon quantification. This workflow performs a DTU analysis on simulated data. It also shows how to use stageR to perform two-stage testing of DTU, a statistical framework to screen at the gene level and then confirm which transcripts within the significant genes show evidence of DTU.

LIANA provides a number of methods and resource for ligand-receptor interaction inference from scRNA-seq data.

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

This package contains a multicore Barnes-Hut implementation of the t-SNE algorithm. The implementation is described here: http://lvdmaaten.github.io/publications/papers/JMLR_2014.pdf.

Python-airr provides a library by the AIRR community to for describing, reporting, storing, and sharing adaptive immune receptor repertoire (AIRR) data, such as sequences of antibodies and T cell receptors (TCRs).

PDBFixer is designed to rectify issues in Protein Data Bank files. Its intuitive interface simplifies the process of resolving problems encountered in PDB files prior to simulation tasks.

HTSJDK is an implementation of a unified Java library for accessing common file formats, such as SAM and VCF, used for high-throughput sequencing (HTS) data. There are also an number of useful utilities for manipulating HTS data.