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

The Filtlong package is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.

Fxtract extracts sequences from a protein or nucleotide fastx (FASTA or FASTQ) file given a subsequence. It uses a simple substring search for basic tasks but can change to using POSIX regular expressions, PCRE, hash lookups or multi-pattern searching as required. By default fxtract looks in the sequence of each record but can also be told to look in the header, comment or quality sections.

ctxcore is part of the SCENIC suite of tools. It provides core functions for pycisTarget and SCENIC.

This package provides Python bindings for lib2bit to access 2bit files with Python.

CrossMap is a program for conversion of genome coordinates or annotation files between different genome assemblies. It supports most commonly used file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.

SeqGL is a group lasso based algorithm to extract transcription factor sequence signals from ChIP, DNase and ATAC-seq profiles. This package presents a method which uses group lasso to discriminate between bound and non bound genomic regions to accurately identify transcription factors bound at the specific regions.

Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can be optionally compressed by gzip.

Pyahocorasick is a fast, memory-efficient library for multi-pattern string search. This means that you can find multiple key strings occurrences at once in some input text.

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.

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

Biosoup is a C++ collection of header-only data structures used for storage and logging in bioinformatics tools.

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

Salad is a schema language for describing JSON or YAML structured linked data documents. Salad schema describes rules for preprocessing, structural validation, and hyperlink checking for documents described by a Salad schema. Salad supports rich data modeling with inheritance, template specialization, object identifiers, object references, documentation generation, code generation, and transformation to RDF. Salad provides a bridge between document and record oriented data modeling and the Semantic Web.

PAIRADISE is a method for detecting allele-specific alternative splicing (ASAS) from RNA-seq data. Unlike conventional approaches that detect ASAS events one sample at a time, PAIRADISE aggregates ASAS signals across multiple individuals in a population. By treating the two alleles of an individual as paired, and multiple individuals sharing a heterozygous SNP as replicates, PAIRADISE formulates ASAS detection as a statistical problem for identifying differential alternative splicing from RNA-seq data with paired replicates.

Forester is a collection of Java libraries for phylogenomics and evolutionary biology research. It includes support for reading, writing, and exporting phylogenetic trees.

Fluff is a Python package that contains several scripts to produce pretty, publication-quality figures for next-generation sequencing experiments.

This helper package implements the HiCMatrix class for the HiCExplorer and pyGenomeTracks packages.

HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. It is a collection of command line programs written in Perl and C++. HOMER was primarily written as a de novo motif discovery algorithm and is well suited for finding 8-20 bp motifs in large scale genomics data. HOMER contains many useful tools for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets.

Circe is a Python package for inferring co-accessibility networks from single-cell ATAC-seq data, using skggm for the graphical lasso and python-scanpy for data processing.

The gdc-client provides several convenience functions over the GDC API which provides general download/upload via HTTPS.

PyLiftover is a library for quick and easy conversion of genomic (point) coordinates between different assemblies.

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.

MUSCLE aims to be a fast and accurate multiple sequence alignment program for nucleotide and protein sequences.