Scanpy is a scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.

The subread package contains the following tools: subread aligner, a general-purpose read aligner; subjunc aligner: detecting exon-exon junctions and mapping RNA-seq reads; featureCounts: counting mapped reads for genomic features; exactSNP: a SNP caller that discovers SNPs by testing signals against local background noises.

BEDOPS is a suite of tools to address common questions raised in genomic studies---mostly with regard to overlap and proximity relationships between data sets. It aims to be scalable and flexible, facilitating the efficient and accurate analysis and management of large-scale genomic data.

BEDOPS provides tools that perform highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for distributing whole-genome analyses across a computational cluster.

This package implements methods for batch correction and integration of scRNA-seq datasets, based on the Seurat anchor-based integration framework. In particular, STACAS is optimized for the integration of heterogeneous datasets with only limited overlap between cell sub-types (e.g. TIL sets of CD8 from tumor with CD8/CD4 T cells from lymphnode), for which the default Seurat alignment methods would tend to over-correct biological differences. The 2.0 version of the package allows the users to incorporate explicit information about cell-types in order to assist the integration process.

This package lets you perform unsupervised clustering of amplicon sequencing data in microbiome studies with the Dirichlet-tree Multinomial Mixtures.

PiGX RNAseq is an analysis pipeline for preprocessing and reporting for RNA sequencing experiments. It is easy to use and produces high quality reports. The inputs are reads files from the sequencing experiment, and a configuration file which describes the experiment. In addition to quality control of the experiment, the pipeline produces a differential expression report comparing samples in an easily configurable manner.

BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is designed for Illumina sequence reads up to 100bp, while the rest two for longer sequences ranged from 70bp to 1Mbp. BWA-MEM and BWA-SW share similar features such as long-read support and split alignment, but BWA-MEM, which is the latest, is generally recommended for high-quality queries as it is faster and more accurate. BWA-MEM also has better performance than BWA-backtrack for 70-100bp Illumina reads.

BayesPrism includes deconvolution and embedding learning modules. The deconvolution module models a prior from cell type-specific expression profiles from scRNA-seq to jointly estimate the posterior distribution of cell type composition and cell type-specific gene expression from bulk RNA-seq expression of tumor samples. The embedding learning module uses Expectation-maximization (EM) to approximate the tumor expression using a linear combination of malignant gene programs while conditional on the inferred expression and fraction of non-malignant cells estimated by the deconvolution module.

ravanan is a CWL implementation that is powered by GNU Guix and provides strong reproducibility guarantees. ravanan provides strong caching of intermediate results so the same step of a workflow is never run twice. ravanan captures logs from every step of the workflow for easy tracing back in case of job failures. ravanan currently runs on single machines and on slurm via its API.

ParDRe is a parallel tool to remove duplicate genetic sequence reads. Duplicate reads can be seen as identical or nearly identical sequences with some mismatches. This tool lets users avoid the analysis of unnecessary reads, reducing the time of subsequent procedures with the dataset (e.g. assemblies, mappings, etc.). The tool is implemented with MPI in order to exploit the parallel capabilities of multicore clusters. It is faster than multithreaded counterparts (end of 2015) for the same number of cores and, thanks to the message-passing technology, it can be executed on clusters.

This package implements bindings for zarr store that are compatible with Bioconductor S4 data structures, namely the DataFrame and DelayedArray. This allows Zarr-backed data to be easily used as data frames with arbitrary sets of columns.

This package provides R miscellaneous utilities for basic data manipulation, debugging, visualization, lsf management, and common mskilab tasks.

CoolBox is a toolkit for visual analysis of genomics data. It aims to be highly compatible with the Python ecosystem, easy to use and highly customizable with a well-designed user interface. It can be used in various visualization situations, for example, to produce high-quality genome track plots or fetch common used genomic data files with a Python script or command line, interactively explore genomic data within Jupyter environment or web browser.

Piranha is a peak-caller for genomic data produced by CLIP-seq and RIP-seq experiments. It takes input in BED or BAM format and identifies regions of statistically significant read enrichment. Additional covariates may optionally be provided to further inform the peak-calling process.

LibSBML is a library to help you read, write, manipulate, translate, and validate SBML files and data streams. The Systems Biology Markup Language (SBML) is an interchange format for computer models of biological processes. SBML is useful for models of metabolism, cell signaling, and more. It continues to be evolved and expanded by an international community.

Bowtie is a fast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).

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.

randfold computes the probability that, for a given sequence, the Minimum Free Energy (MFE) of the secondary structure is different from MFE computed with random sequences.

VSEARCH supports DNA sequence searching, clustering, chimera detection, dereplication, pairwise alignment, shuffling, subsampling, sorting and masking. The tool takes advantage of parallelism in the form of SIMD vectorization as well as multiple threads to perform accurate alignments at high speed. VSEARCH uses an optimal global aligner (full dynamic programming Needleman-Wunsch).

PhyML is a software package that uses modern statistical approaches to analyse alignments of nucleotide or amino acid sequences in a phylogenetic framework. The main tool in this package builds phylogenies under the maximum likelihood criterion. It implements a large number of substitution models coupled with efficient options to search the space of phylogenetic tree topologies. codePhyREX fits the spatial-Lambda-Fleming-Viot model to geo-referenced genetic data. This model is similar to the structured coalescent but assumes that individuals are distributed along a spatial continuum rather than discrete demes. PhyREX can be used to estimate population densities and rates of dispersal. Its output can be processed by treeannotator (from the BEAST package) as well as SPREAD.

wfmash is a DNA sequence read mapper based on mash distances and the wavefront alignment algorithm. It is a fork of MashMap that implements base-level alignment via the wflign tiled wavefront global alignment algorithm. It completes MashMap with a high-performance alignment module capable of computing base-level alignments for very large sequences.

This package aims to simplify working with genomic region / interval data by providing a common interface that lets you access a wide selection of file types and formats for handling genomic region data---all using the same syntax.

This package provides a deconvolution based on Single Nucleotide Position (SNP) for multiplexed scRNA-seq data. The name vireo stand for Variational Inference for Reconstructing Ensemble Origin by expressed SNPs in multiplexed scRNA-seq data and follows the clone identification from single-cell data named cardelino.

MinCED is a program to find Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) in DNA sequences. It can be used for unassembled metagenomic reads, but is mainly designed for full genomes and assembled metagenomic sequence.