CLIPper is a tool to define peaks in CLIP-seq datasets.

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

deMULTIplex is an R package for analyzing single-cell RNA sequencing data generated with the MULTI-seq sample multiplexing method. The package includes software to

1. Convert raw MULTI-seq sample barcode library FASTQs into a sample barcode UMI count matrix, and

2. Classify cell barcodes into sample barcode groups.

CodingQuarry is a highly accurate, self-training GHMM fungal gene predictor designed to work with assembled, aligned RNA-seq transcripts.

SeqAn is a C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. It contains algorithms and data structures for string representation and their manipulation, online and indexed string search, efficient I/O of bioinformatics file formats, sequence alignment, and more.

Samtools implements various utilities for post-processing nucleotide sequence alignments in the SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction with bcftools), and a simple alignment viewer.

Cell2cell is a Python library for cell communication analysis. This is a method to calculate, visualize and analyze communication between cell types. Cell2cell is suitable for single-cell RNA sequencing (scRNA-seq) data.

This package provides a concrete implementation of the fast5 file schema using the generic h5py library, plain-named methods to interact with and reflect the fast5 file schema, and tools to convert between multi_read and single_read formats.

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.

The NCBI-VDB library implements a highly compressed columnar data warehousing engine that is most often used to store genetic information. Databases are stored in a portable image within the file system, and can be accessed/downloaded on demand across HTTP.

Maxent is a stand-alone Java application for modelling species geographic distributions.

This package provides data for the SeuratExtend tool.

ChIPKernels is an R package for building different string kernels used for DNA Sequence analysis. A dictionary of the desired kernel must be built and this dictionary can be used for determining kernels for DNA Sequences.

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).

This is a package that lets you process UMI-4C data from scratch to produce nice plots.

FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.

GSEApy is a Python/Rust implementation for GSEA and wrapper for Enrichr. GSEApy can be used for RNA-seq, ChIP-seq, Microarray data. It can be used for convenient GO enrichment and to produce publication quality figures in Python.

PLINK is a whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data). Through integration with gPLINK and Haploview, there is some support for the subsequent visualization, annotation and storage of results.

Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq). It analyzes alignment files generated following the assay and produces a file detailing peaks of significant enrichment.

This package provides accelerated functions for the CIRI toolkit. It also provides the ccs executable to scan for circular consensus sequences.

libmaus2 is a collection of data structures and algorithms. It contains:

• I/O classes (single byte and UTF-8);

• bitio classes (input, output and various forms of bit level manipulation);

• text indexing classes (suffix and LCP array, fulltext and minute (FM), etc.);

• BAM sequence alignment files input/output (simple and collating); and many lower level support classes.

PRINSEQ is a bioinformatics tool to help you preprocess your genomic or metagenomic sequence data in FASTA or FASTQ formats. The tool is written in Perl and can be helpful if you want to filter, reformat, or trim your sequence data. It also generates basic statistics for your sequences.

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.

TADbit is a complete Python library to deal with all steps to analyze, model, and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models.