Evolutionary Transcriptomics with R

Mirror of Bioconductor's CAGEr package repository

⏳ Online graphical interface to explore age-related gene expression alterations in 49 GTEx human tissues

pcaExplorer - Interactive exploration of Principal Components of Samples and Genes in RNA-seq data

Enjoy your transcriptomic data and analysis responsibly - like sipping a cocktail

Analysis of single and comparative transcriptomes

GET_HOMOLOGUES: a versatile software package for pan-genome analysis

A genome annotation pipeline that use short and long sequencing reads alignments from animal genomes

An application for exploring and visualizing differential gene expression data created with DESeq2

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

A Python library to visualize and analyze long-read transcriptomes

Nanopore sequence read simulator

Pipeline for HiCAR data, a robust and sensitive multi-omic co-assay for simultaneous measurement of transcriptome, chromatin accessibility and cis-regulatory chromatin contacts.

UNDER DEVELOPMENT--- Analysis of long non-coding RNAs from RNA-seq datasets

Inferring Transcript Phylogenies from Transcript Ortholog Clusters

Reference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing

Neural signal propagation atlas (Randi et al.), genome (WormBase), single-cell transcriptome (Taylor et al.), neuropeptide/GPCR deorphanization (Beets et al.), monoaminergic connectome (Bentley et al.), and chemical-synapse sign predictions (Fenyves et al.) all in one place. Read the docs: https://francescorandi.github.io/wormneuroatlas/

Code for MERFISH analysis

Technology agnostic long read analysis pipeline for transcriptomes

TrendCatcher is an open source R-package that allows users to systematically analyze and visualize time course data. Please cite "Temporal transcriptomic analysis using TrendCatcher identifies early and persistent neutrophil activation in severe COVID-19" by Xinge Wang et al published in JCI Insight (2022) - https://insight.jci.org/articles/view…