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

A tandem repeat in DNA is two or more adjacent, approximate copies of a pattern of nucleotides. Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences. In order to use the program, the user submits a sequence in FASTA format. The output consists of two files: a repeat table file and an alignment file. Submitted sequences may be of arbitrary length. Repeats with pattern size in the range from 1 to 2000 bases are detected.

VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.

Parabam is a tool for processing sequencing files in parallel. It uses Python's native multiprocessing framework to apply a user defined rule on an input file.

ReadWriter is a set of R functions to read and write files conveniently.

TSIS is used for detecting transcript isoform switches in time-series data. Transcript isoform switches occur when a pair of alternatively spliced isoforms reverse the order of their relative expression levels. TSIS characterizes the transcript switch by defining the isoform switch time-points for any pair of transcript isoforms within a gene. In addition, this tool describes the switch using five different features or metrics. Also it filters the results with user’s specifications and visualizes the results using different plots for the user to examine further details of the switches.

The phylo module provides a biojava interface layer to the forester phylogenomics library for constructing phylogenetic trees.

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 package provides a method to detect and enable removal of doublets from single-cell RNA-sequencing.

Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database. Typical use cases include:

1. mapping PacBio or Oxford Nanopore genomic reads to the human genome;

2. finding overlaps between long reads with error rate up to ~15%;

3. splice-aware alignment of PacBio Iso-Seq or Nanopore cDNA or Direct RNA reads against a reference genome;

4. aligning Illumina single- or paired-end reads;

5. assembly-to-assembly alignment;

6. full-genome alignment between two closely related species with divergence below ~15%.

Mudata is a Python package for multi-omics data analysis. It is designed to provide functionality to load, process, and store multimodal omics data.

This package provides extra utility functions to perform common tasks in the analysis of omics data, leveraging and enhancing features provided by Bioconductor packages.

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.

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.

RAxML is a tool for phylogenetic analysis and post-analysis of large phylogenies.

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

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.

This package provides an R API and htmlwidget facilitating interactive visualization of spatial single-cell data with Vitessce. The R API contains classes and functions for loading single-cell data stored in compatible on-disk formats. The htmlwidget is a wrapper around the Vitessce JavaScript library and can be used in the Viewer tab of RStudio or Shiny apps.

DoubletFinder identifies doublets by generating artificial doublets from existing scRNA-seq data and defining which real cells preferentially co-localize with artificial doublets in gene expression space. Other DoubletFinder package functions are used for fitting DoubletFinder to different scRNA-seq datasets. For example, ideal DoubletFinder performance in real-world contexts requires optimal pK selection and homotypic doublet proportion estimation. pK selection is achieved using pN-pK parameter sweeps and maxima identification in mean-variance-normalized bimodality coefficient distributions. Homotypic doublet proportion estimation is achieved by finding the sum of squared cell annotation frequencies.

The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.

Next-Generation sequencing machines usually produce FASTA or FASTQ files, containing multiple short-reads sequences. The main processing of such FASTA/FASTQ files is mapping the sequences to reference genomes. However, it is sometimes more productive to preprocess the files before mapping the sequences to the genome---manipulating the sequences to produce better mapping results. The FASTX-Toolkit tools perform some of these preprocessing tasks.

WhatsHap is software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. It is especially suitable for long reads, but works also well with short reads.

This package provides a framework to process and analyze data from high-throughput sequencing (HTS) assays

Vcflib provides methods to manipulate and interpret sequence variation as it can be described by VCF. It is both an API for parsing and operating on records of genomic variation as it can be described by the VCF format, and a collection of command-line utilities for executing complex manipulations on VCF files.

This package provides data for the book "Computational Genomics with R".