Gene transcripts Tools

Alevin-fry-atac is a tool for rapid and memory-frugal mapping of single-cell ATAC-seq data utilizing virtual colors for accurate genomic pseudoalignment. It is freely available under a BSD 3-clause license and integrated into piscem and simpleaf.

Arriba is a command-line tool to detect gene fusions from RNA-Seq data based on the STAR aligner. In addition to fusions, it can detect exon duplications/inversions and truncations of genes (i.e., breakpoints in introns and intergenic regions). Arriba is the winner of the DREAM SMC-RNA Challenge.

AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally.

Genome-wide annotation of circRNAs and their alternative back-splicing/splicing.

Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.

Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads.

Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well.

Fast fusion detection using kallisto

Web application for convenient identification of evolutionary conserved protein coding regions.

TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.

Bustools is a program for manipulating BUS files for single cell RNA-Seq datasets.

CellRank is a package for mapping the fate of single cells in diverse scenarios, including perturbations such as regeneration or disease, for which direction is unknown. The approach combines the robustness of trajectory inference with directional information from RNA velocity, derived from ratios of spliced to unspliced reads. CellRank takes into account both the gradual and stochastic nature of cellular fate decisions, as well as uncertainty in RNA velocity vectors

CellRank is a package for mapping the fate of single cells in diverse scenarios, including perturbations such as regeneration or disease, for which direction is unknown. The approach combines the robustness of trajectory inference with directional information from RNA velocity, derived from ratios of spliced to unspliced reads. CellRank takes into account both the gradual and stochastic nature of cellular fate decisions, as well as uncertainty in RNA velocity vectors

CICERO (Clipped-reads Extended for RNA Optimization) is an assembly-based algorithm to detect diverse classes of driver gene fusions from RNA-seq. It is a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data.

CirComPara2 is a computational pipeline to detect, quantify, and correlate expression of linear and circular RNAs from RNA-seq data that combines multiple circRNA-detection methods.

clearCNV is a bioinformatics software package designed to detect Copy Number Variations (CNVs) in targeted Next-Generation Sequencing (NGS) panel data. It is specifically built to handle ambiguity and noise, making it effective at identifying larger multi-exon CNVs that might otherwise be missed.

A rapid, high-throughput, and variant-aware in silico off-target site identification for CRISPR genome editing. Tool package to perform in-silico CRISPR analysis and assessment. CRISPRitz is a software package containing 5 different tools dedicated to perform predictive analysis and result assessement on CRISPR/Cas experiments.

An R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages.