Nanopore sequence read simulator

Technology agnostic long read analysis pipeline for transcriptomes

Merging, Annotation, Validation, and Illustration of Structural variants

De novo clustering of long transcript reads into genes

de novo assembly of RNA-seq data using ABySS

Demultiplexing and debarcoding tool designed for LR-Split-seq data.

Annotated Genome Optimization Using Transcriptome Information

Derives consensus sequences from a set of long noisy reads by clustering and error correction.

Emending Alignment of Spliced Transcript Reads

Snakemake workflow to run transdecoder + trinotate

We use two kinds of neural networks: Multilayer Perceptron (MLP) and Recurrent Neural Network (RNN) to predict the single-cell cycle stage based on transcriptome data.

orthomap is a python package to extract orthologous maps (in other words the evolutionary age of a given orthologous group) from OrthoFinder/eggNOG results. Orthomap results (gene ages per orthogroup) can be further used to calculate weigthed expression data (transcriptome evolutionary index) from scRNA sequencing objects.

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/

Escherichia coli Transcriptome Assembly from a Compendium of RNA-seq Data Sets

Get exons from a transcriptome and raw genomic reads using abyss-bloom and bedtools

Use scaffold realigning strategy to detect the recurrence of a list fusion transcripts across samples

Simulating RNA-Seq reads from transcriptome to test software (e.g. for Drop-Seq singleCell software)

SIMulator for Long read transcriptome Analysis with RNA DecaY model

Select best protein codeing genes from models Generated from MAKER2, Cufflinks and any de novo assembling programs. Previously called MCOT, with this publication (http://www.sciencedirect.com/science/article/pii/S0965174815000144).

A snakemake workflow for performing de novo transcriptome assembly, quality assessment and transcript quantification.