NanoSV is a software package that can be used to identify structural genomic variations in long-read sequencing data, such as data produced by Oxford Nanopore Technologies’ MinION, GridION or PromethION instruments, or Pacific Biosciences RSII or Sequel sequencers.

The Shaman package implements functions for resampling Hi-C matrices in order to generate expected contact distributions given constraints on marginal coverage and contact-distance probability distributions. The package also provides support for visualizing normalized matrices and statistical analysis of contact distributions around selected landmarks.

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.

gffcompare is a tool that can:

1. compare and evaluate the accuracy of RNA-Seq transcript assemblers (Cufflinks, Stringtie);

2. collapse (merge) duplicate transcripts from multiple GTF/GFF3 files (e.g. resulted from assembly of different samples);

3. classify transcripts from one or multiple GTF/GFF3 files as they relate to reference transcripts provided in a annotation file (also in GTF/GFF3 format).

This package provides basic routines for estimation of gene-specific transcriptional derivatives and visualization of the resulting velocity patterns.

LIANA provides a number of methods and resource for ligand-receptor interaction inference from scRNA-seq data.

The ZarrArray package leverages the Rarr package to bring Zarr datasets in R as DelayedArray objects. The main class in the package is the ZarrArray class. A ZarrArray object is an array-like object that represents a Zarr dataset in R. ZarrArray objects are DelayedArray derivatives and therefore support all operations (delayed or block-processed) supported by DelayedArray objects.

This package is tools for analysing intercellular and intracellular signaling from single cell RNA-seq (scRNA-seq) data.

The WiggleTools package allows genomewide data files to be manipulated as numerical functions, equipped with all the standard functional analysis operators (sum, product, product by a scalar, comparators), and derived statistics (mean, median, variance, stddev, t-test, Wilcoxon's rank sum test, etc).

This package provides an object for plotting GRanges, RleList, UCSC file formats, and ffTrack objects in multi-track panels.

F-Seq is a software package that generates a continuous tag sequence density estimation allowing identification of biologically meaningful sites such as transcription factor binding sites (ChIP-seq) or regions of open chromatin (DNase-seq). Output can be displayed directly in the UCSC Genome Browser.

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.

Deacon filters DNA sequences in FASTA/Q files and streams using SIMD-accelerated minimizer comparison with query sequence(s), emitting either matching sequences (search mode), or sequences without matches (deplete mode). Sequences match when they share enough distinct minimizers with the indexed query to exceed chosen absolute and relative thresholds. Query size has little impact on filtering speed, enabling ultrafast search and depletion with gene-, genome- and pangenome-scale queries using a laptop.

This package implements two functions:

• pairwise.adonis is a wrapper function for multilevel pairwise comparison using adonis2 from package vegan. The function returns adjusted p-values using p.adjust(). It does not accept interaction between factors neither strata.

• pairwise.adonis2 accepts a model formula like in adonis from vegan. You can use interactions between factors and define strata to constrain permutations. For pairwise comparison a list of unique pairwise combination of factors is produced.

LoFreq is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or base/indel alignment uncertainty), which are usually ignored by other methods or only used for filtering.

This package provides a framework for the analysis and exploration of single-cell chromatin data. The Signac package contains functions for quantifying single-cell chromatin data, computing per-cell quality control metrics, dimension reduction and normalization, visualization, and DNA sequence motif analysis.

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.

EpiScanpy is a toolkit to analyse single-cell open chromatin (scATAC-seq) and single-cell DNA methylation (for example scBS-seq) data. EpiScanpy is the epigenomic extension of the very popular scRNA-seq analysis tool Scanpy (Genome Biology, 2018).

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

This package generates a Miami plot with centered chromosome labels. The output is a ggplot2 object. Users can specify which data they want plotted on top vs. bottom, whether to display significance line(s), what colors to give chromosomes, and what points to label.

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.

ShoRAH is a project for the analysis of next generation sequencing data. It is designed to analyse genetically heterogeneous samples. Its tools provide error correction, haplotype reconstruction and estimation of the frequency of the different genetic variants present in a mixed sample.

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.

Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data. It was developed for the use in a clinical research setting. Therefore, short runtimes and high sensitivity were important design criteria. It is based on the fast STAR aligner and the post-alignment runtime is typically just around two minutes. In contrast to many other fusion detection tools which build on STAR, Arriba does not require to reduce the alignIntronMax parameter of STAR to detect small deletions.