Transcriptomics Tools

This R package provide functions that are used in the BREW3R workflow. This mainly contains a function that extend a gtf as GRanges using information from another gtf (also as GRanges). The process allows to extend gene annotation without increasing the overlap between gene ids.

Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs.

It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network.

Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment.

Cufflinks assembles transcripts and estimates their abundances in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one.

Collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.

Genomic Mapping and Alignment Program for mRNA and EST Sequences.

GOATools is a Python library for parsing and analyzing Gene Ontology (GO) annotations, enabling statistical analysis of GO term enrichment, visualization of GO hierarchies, and propagation of GO annotations across biological datasets.

A comprehensive package for performing gene set enrichment analysis in Python.

A software package for analyzing various features of gene models.

GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases.

GimmeMotifs is a de novo motif prediction pipeline, especially suited for ChIP-seq datasets. It incorporates several existing motif prediction algorithms in an ensemble method to predict motifs and clusters these motifs using the WIC similarity scoring metric.

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

IsoQuant is a tool for the genome-based analysis of long RNA reads, such as PacBio or Oxford Nanopores.

IsoSeq v3 contains the newest tools to identify transcripts in PacBio single-molecule sequencing data. Starting in SMRT Link v6.0.0, those tools power the IsoSeq GUI-based analysis application. A composable workflow of existing tools and algorithms, combined with a new clustering technique.

KisSplice is a software that enables to analyse RNA-seq data with or without a reference genome.

To identify cis-NATs using ssRNA-seq, a new computational method was developed based on model comparison that incorporates the inherent variable efficiency of generating perfectly strand-specific libraries.

Ultrafast universal RNA-seq data aligner.

seq2HLA is a computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class.

Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data. Seurat aims to enable users to identify and interpret sources of heterogeneity from single-cell transcriptomic measurements, and to integrate diverse types of single-cell data.

Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus.

Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads.

Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.

AGFusion (pronounced 'A G Fusion') is a python package for annotating gene fusions from the human or mouse genomes.

Anvi’o is an open-source, community-driven analysis and visualization platform for microbial ‘omics. It brings together many aspects of today’s cutting-edge strategies including genomics, metagenomics, metatranscriptomics, pangenomics, metapangenomics, phylogenomics, and microbial population genetics in an integrated and easy-to-use fashion through extensive interactive visualization capabilities.

ASGAL (Alternative Splicing Graph ALigner) is a tool for detecting the alternative splicing events expressed in a RNA-Seq sample with respect to a gene annotation. The main idea behind ASGAL is the following one: the alternative splicing events can be detected by aligning the RNA-Seq reads against the splicing graph of the gene.

The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq 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.

CIRIquant is a comprehensive analysis pipeline for circRNA detection and quantification in RNA-Seq data

Drop-seq is a high-throughput, droplet-based single-cell RNA sequencing (scRNA-seq) technology that allows for genome-wide expression profiling of thousands of individual cells simultaneously. It works by encapsulating single cells and barcoded microbeads into nanoliter-sized aqueous droplets in oil using a microfluidic device.

Pipeline for estimating molecular count matrices for droplet-based single-cell RNA-seq measurements. I

Set of Linux utilities to validate and manipulate fastq files. It also includes a set of programs to preprocess barcodes (namely UMIs, cells and samples), add the barcodes as tags in BAM files and count UMIs.

Command line utility for manipulating FASTQ files

Program for comparing, annotating, merging and tracking transcripts in GFF files.

Program for filtering, converting and manipulating GFF files

Python package for working with GFF and GTF files. It allows operations which would be complicated or time-consuming using a text-file-only approach.

A program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.

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.