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.

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

libmaus2 is a collection of data structures and algorithms. It contains:

• I/O classes (single byte and UTF-8);

• bitio classes (input, output and various forms of bit level manipulation);

• text indexing classes (suffix and LCP array, fulltext and minute (FM), etc.);

• BAM sequence alignment files input/output (simple and collating); and many lower level support classes.

Several studies focus on the inference of developmental and response trajectories from single cell RNA-Seq (scRNA-Seq) data. A number of computational methods, often referred to as pseudo-time ordering, have been developed for this task. CRISPR has also been used to reconstruct lineage trees by inserting random mutations. The tbsp package implements an alternative method to detect significant, cell type specific sequence mutations from scRNA-Seq data.

This package implements methods to project single-cell RNA-seq data onto a reference atlas, enabling interpretation of unknown cell transcriptomic states in the the context of known, reference states.

This library contains the genomics components of the Bio++ sequence library. It is part of the Bio++ project.

This package Copynumber KAryotyping of Tumors infers genomic copy number and subclonal structure of human tumors using integrative Bayesian approaches to identify genome-wide aneuploidy at 5MB resolution in single cells data. It separates tumor cells and tumor subclones from normal cells using high-throughput sc-RNAseq data.

Proteinortho is a tool to detect orthologous genes across different species. For doing so, it compares similarities of given gene sequences and clusters them to find significant groups. The algorithm was designed to handle large-scale data and can be applied to hundreds of species at once.

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.

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

This package provides a C library for parsing local and remote BigWig files.

This package provides an accurate VCF/GFF3/GTF LiftOver tool for new genome assemblies.

Megahit is a fast and memory-efficient NGS assembler. It is optimized for metagenomes, but also works well on generic single genome assembly (small or mammalian size) and single-cell assembly.

This package provides TagGD barcode demultiplexing utilities for Spatial Transcriptomics data.

Savvy is the official C++ interface for the SAV file format and offers seamless support for BCF and VCF files.

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.

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.

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

Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. This package provides command line tools using the Bio++ library.

inStrain is a Python program for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification.

Sylamer is a system for finding significantly over or under-represented words in sequences according to a sorted gene list. Typically it is used to find significant enrichment or depletion of microRNA or siRNA seed sequences from microarray expression data. Sylamer is extremely fast and can be applied to genome-wide datasets with ease. Results are plotted in terms of a significance landscape plot. These plots show significance profiles for each word studied across the sorted genelist.

Entrez Direct (EDirect) is a method for accessing the National Center for Biotechnology Information's (NCBI) set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a terminal. Functions take search terms from command-line arguments. Individual operations are combined to build multi-step queries. Record retrieval and formatting normally complete the process.

EDirect also provides an argument-driven function that simplifies the extraction of data from document summaries or other results that are returned in structured XML format. This can eliminate the need for writing custom software to answer ad hoc questions.

PDBFixer is designed to rectify issues in Protein Data Bank files. Its intuitive interface simplifies the process of resolving problems encountered in PDB files prior to simulation tasks.

This package aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot: bigwig, bed (many options), bedgraph, links (represented as arcs), and Hi-C matrices. pyGenomeTracks can make plots with or without Hi-C data.