DelayedArray based image operations.

This package provides a companion annotation file to the IlluminaHumanMethylationEPICmanifest package based on the same annotation 1.0B5.

The HH-suite is a software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).

CodeAndRoll2 is a set of more than 130 productivity functions. These functions are used by MarkdownReports, ggExpress, and SeuratUtils.

This package provides a Python client for BioThings API services.

BamTools provides both a C++ API and a command-line toolkit for handling BAM files.

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

Centrifuge is a microbial classification engine that enables rapid, accurate and sensitive labeling of reads and quantification of species on desktop computers. The system uses an indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. Centrifuge requires a relatively small index (4.7 GB for all complete bacterial and viral genomes plus the human genome) and classifies sequences at very high speed, allowing it to process the millions of reads from a typical high-throughput DNA sequencing run within a few minutes.

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.

python-cwl-upgrader is a standalone upgrader for CWL documents from version draft-3, v1.0, and v1.1 to v1.2.

HTSlib is a C library for reading/writing high-throughput sequencing data. It also provides the bgzip, htsfile, and tabix utilities.

Scallop is a reference-based transcript assembler. Scallop features its high accuracy in assembling multi-exon transcripts as well as lowly expressed transcripts.

This package provides a tool for identifying and removing doublets in single-cell RNA-seq data.

EMBOSS is the "European Molecular Biology Open Software Suite". EMBOSS is an analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. It also provides a number of libraries for the development of software in the field of molecular biology. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole.

Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. This library provides phylogenetics-related modules.

Bowtie 2 is a fast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.

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.

The SRA Toolkit from NCBI is a collection of tools and libraries for reading of sequencing files from the Sequence Read Archive (SRA) database and writing files into the .sra format.

MAGIC is an interactive tool to impute missing values in single-cell sequencing data and to restore the structure of the data. It also provides data pre-processing functionality such as dimensionality reduction and gene expression visualization.

hdWGCNA is an R package for performing weighted gene co-expression network analysis in high dimensional -omics such as single-cell RNA-seq or spatial transcriptomics.

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.

This is a fast parser for minimap2 PAF (Pairwise mApping Format) files.

This package provides different statistical methods to extract biological activities from omics data within a unified framework.

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.