This helper package implements the HiCMatrix class for the HiCExplorer and pyGenomeTracks packages.

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.

The Spliced Transcripts Alignment to a Reference (STAR) software is based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences.

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 detects naive associations between omics features and metadata in cross-sectional data-sets using non-parametric tests. In a second step, confounding effects between metadata associated to the same omics feature are detected and labeled using nested post-hoc model comparison tests. The generated output can be graphically summarized using the built-in plotting function.

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.

This package provides a GFF/GTF file parsing utility providing format conversions, region filtering, FASTA sequence extraction and more.

InDelFixer is a sensitive aligner for 454, Illumina and PacBio data, employing a full Smith-Waterman alignment against a reference. This Java command line application aligns Next-Generation Sequencing (NGS) and third-generation reads to a set of reference sequences, by a prior fast k-mer matching and removes indels, causing frame shifts. In addition, only a specific region can be considered. An iterative refinement of the alignment can be performed, by alignment against the consensus sequence with wobbles. The output is in SAM format.

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

Anglemania extracts genes from multi-batch scRNA-seq experiments for downstream dataset integration. It improves conventional usage of highly-variable genes for integration tasks.

DNA Features Viewer is a Python library to visualize DNA features, e.g. from GenBank or Gff files, or Biopython SeqRecords.

Trim Galore! is a wrapper script to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files.

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.

Mantis is a space-efficient data structure that can be used to index thousands of raw-read genomics experiments and facilitate large-scale sequence searches on those experiments. Mantis uses counting quotient filters instead of Bloom filters, enabling rapid index builds and queries, small indexes, and exact results, i.e., no false positives or negatives. Furthermore, Mantis is also a colored de Bruijn graph representation, so it supports fast graph traversal and other topological analyses in addition to large-scale sequence-level searches.

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

SlamDunk is a fully automated tool for automated, robust, scalable and reproducible SLAMseq data analysis. Diagnostic plotting features and a MultiQC plugin will make your SLAMseq data ready for immediate QA and interpretation.

This package implements FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. FLAIR has primarily been used for nanopore cDNA, native RNA, and PacBio sequencing reads.

This program compares version strings. It intends to be a replacement for strverscmp.

The preseq package is aimed at predicting and estimating the complexity of a genomic sequencing library, equivalent to predicting and estimating the number of redundant reads from a given sequencing depth and how many will be expected from additional sequencing using an initial sequencing experiment. The estimates can then be used to examine the utility of further sequencing, optimize the sequencing depth, or to screen multiple libraries to avoid low complexity samples.

This package provides a package that makes it easy to implement sankey, alluvial and sankey bump plots in ggplot2.

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.

The store package provides a number of data store types that are useful for bioinformatic analysis.

This package provides a fast and accurate analysis toolkit for single cell ATAC-seq (Assay for transposase-accessible chromatin using sequencing). Single cell ATAC-seq can resolve the heterogeneity of a complex tissue and reveal cell-type specific regulatory landscapes. However, the exceeding data sparsity has posed unique challenges for the data analysis. This package r-snapatac is an end-to-end bioinformatics pipeline for analyzing large- scale single cell ATAC-seq data which includes quality control, normalization, clustering analysis, differential analysis, motif inference and exploration of single cell ATAC-seq sequencing data.

t-Stochastic Neighborhood Embedding (t-SNE) is a method for dimensionality reduction and visualization of high dimensional datasets. A popular implementation of t-SNE uses the Barnes-Hut algorithm to approximate the gradient at each iteration of gradient descent. This implementation differs in these ways:

• Instead of approximating the N-body simulation using Barnes-Hut, we interpolate onto an equispaced grid and use FFT to perform the convolution.

• Instead of computing nearest neighbors using vantage-point trees, we approximate nearest neighbors using the Annoy library. The neighbor lookups are multithreaded to take advantage of machines with multiple cores.