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

SCENIC (Single-cell regulatory network inference and clustering) is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.

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.

Megahit is a fast and memory-efficient NGS assembler. It is optimized for metagenomes, but also works well on generic single genome assembly (small or mammalian size) and single-cell assembly.

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.

This package is designed to streamline scATAC analyses in R.

This package is analyzing TCR and BCR sequences using unselected RNA sequencing data, profiled from fluid and solid tissues, including tumors. TRUST4 performs de novo assembly on V, J, C genes including the hypervariable CDR3 and reports consensus contigs of BCR/TCR sequences. TRUST4 then realigns the contigs to IMGT reference gene sequences to identify the corresponding gene and CDR3 details. TRUST4 supports both single-end and paired-end bulk or single-cell sequencing data with any read length.

Picard is a set of Java command line tools for manipulating high-throughput sequencing (HTS) data and formats. Picard is implemented using the HTSJDK Java library to support accessing file formats that are commonly used for high-throughput sequencing data such as SAM, BAM, CRAM and VCF.

This package offers a flexible statistical simulator for scRNA-seq data. It can generate data that captures gene correlation. Additionally, it allows for varying the number of cells and sequencing depth.

Splicekit is a modular platform for splicing analysis from short-read RNA-seq datasets. The platform also integrates pybio for genomic operations and scanRBP for RNA-protein binding studies. The whole analysis is self-contained (one single directory) and the platform is written in Python, in a modular way.

Sleuth is a program for differential analysis of RNA-Seq data. It makes use of quantification uncertainty estimates obtained via Kallisto for accurate differential analysis of isoforms or genes, allows testing in the context of experiments with complex designs, and supports interactive exploratory data analysis via sleuth live.

MultiQC is a tool to aggregate bioinformatics results across many samples into a single report. It contains modules for a large number of common bioinformatics tools.

This package is used for cell type identification in spatial transcriptomics. It also handles cell type-specific differential expression.

This package provides a a transcriptomic-based framework to dissect cell communication in a global manner. It integrates an original expert-curated database of ligand-receptor interactions taking into account multiple subunits expression. Based on transcriptomic profiles (gene expression), this package computes communication scores between cells and provides several visualization modes that can be helpful to dig into cell-cell interaction mechanism and extend biological knowledge.

This package contains the Battenberg R package for subclonal copy number estimation, as described by Nik-Zainal et al.

This package addresses the challenge of handling large amounts of data that are now routinely generated from DNA sequencing centers. deepTools contains useful modules to process the mapped reads data for multiple quality checks, creating normalized coverage files in standard bedGraph and bigWig file formats, that allow comparison between different files. Finally, using such normalized and standardized files, deepTools can create many publication-ready visualizations to identify enrichments and for functional annotations of the genome.

Pairtools is a simple and fast command-line framework to process sequencing data from a Hi-C experiment. Process pair-end sequence alignments and perform the following operations:

• detect ligation junctions (a.k.a. Hi-C pairs) in aligned paired-end sequences of Hi-C DNA molecules

• sort .pairs files for downstream analyses

• detect, tag and remove PCR/optical duplicates

• generate extensive statistics of Hi-C datasets

• select Hi-C pairs given flexibly defined criteria

• restore .sam alignments from Hi-C pairs.

Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names. It also adds a few built-in functions and a command line option to use TAB as the input/output delimiter. When the new functionality is not used, bioawk is intended to behave exactly the same as the original BWK awk.

This package provides a toolbox to process, analyze and visualize spatial single-cell expression data.

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.

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.

PiGx BSseq is a data processing pipeline for raw fastq read data of bisulfite experiments; it produces reports on aggregate methylation and coverage and can be used to produce information on differential methylation and segmentation.

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.

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