This package contains gatingTemplates, example fcs files and compensation controls for use in CytoExploreR.

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.

Segemehl is software to map short sequencer reads to reference genomes. Segemehl implements a matching strategy based on enhanced suffix arrays (ESA). It accepts fasta and fastq queries (gzip'ed and bgzip'ed). In addition to the alignment of reads from standard DNA- and RNA-seq protocols, it also allows the mapping of bisulfite converted reads (Lister and Cokus) and implements a split read mapping strategy. The output of segemehl is a SAM or BAM formatted alignment file.

BWA-PSSM is a probabilistic short genomic sequence read aligner based on the use of position specific scoring matrices (PSSM). Like many of the existing aligners it is fast and sensitive. Unlike most other aligners, however, it is also adaptible in the sense that one can direct the alignment based on known biases within the data set. It is coded as a modification of the original BWA alignment program and shares the genome index structure as well as many of the command line options.

JAMM is a peak finder for next generation sequencing datasets (ChIP-Seq, ATAC-Seq, DNase-Seq, etc.) that can integrate replicates and assign peak boundaries accurately. JAMM is applicable to both broad and narrow datasets.

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

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

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.

Cyvcf2 is a Cython wrapper around htslib built for fast parsing of Variant Call Format (VCF) files.

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

Pypairix is a Python module for fast querying on a pairix-indexed bgzipped text file that contains a pair of genomic coordinates per line.

CellTypist is an automated cell type annotation tool for scRNA-seq datasets on the basis of logistic regression classifiers optimised by the stochastic gradient descent algorithm. CellTypist allows for cell prediction using either built-in (with a current focus on immune sub-populations) or custom models, in order to assist in the accurate classification of different cell types and subtypes.

LAMMPS is a classical molecular dynamics simulator designed to run efficiently on parallel computers. LAMMPS has potentials for solid-state materials (metals, semiconductors), soft matter (biomolecules, polymers), and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale.

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.

This package contains a multicore Barnes-Hut implementation of the t-SNE algorithm. The implementation is described here: http://lvdmaaten.github.io/publications/papers/JMLR_2014.pdf.

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

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.

This R package lets you estimate signatures of mutational processes and their activities on mutation count data. Starting from a set of single-nucleotide variants (SNVs), it allows both estimation of the exposure of samples to predefined mutational signatures (including whether the signatures are present at all), and identification of signatures de novo from the mutation counts.

BioJava is a project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats, reference implementations of popular algorithms, and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics.

This package provides the core libraries.

This package provides a simple web interface for the RNA-centric annotation system (RCAS).

HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).

SortMeRNA is a biological sequence analysis tool for filtering, mapping and OTU picking of NGS reads. The core algorithm is based on approximate seeds and allows for fast and sensitive analyses of nucleotide sequences. The main application of SortMeRNA is filtering rRNA from metatranscriptomic data.

Grassroots DICOM (GDCM) is an implementation of the DICOM standard designed to be open source so that researchers may access clinical data directly. GDCM includes a file format definition and a network communications protocol, both of which should be extended to provide a full set of tools for a researcher or small medical imaging vendor to interface with an existing medical database.

This package implements scalable gene regulatory network inference using tree-based ensemble regressors.