Nanopore sequence read simulator
-
Updated
Aug 17, 2024 - Python
Nanopore sequence read simulator
Technology agnostic long read analysis pipeline for transcriptomes
de novo assembly of RNA-seq data using ABySS
Merging, Annotation, Validation, and Illustration of Structural variants
De novo clustering of long transcript reads into genes
Demultiplexing and debarcoding tool designed for LR-Split-seq data.
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/
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.
Snakemake workflow to run transdecoder + trinotate
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
Derives consensus sequences from a set of long noisy reads by clustering and error correction.
Simulating RNA-Seq reads from transcriptome to test software (e.g. for Drop-Seq singleCell software)
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.
Snakemake pipeline to validate exfi's performance
Escherichia coli Transcriptome Assembly from a Compendium of RNA-seq Data Sets
SIMulator for Long read transcriptome Analysis with RNA DecaY model
A snakemake workflow for performing de novo transcriptome assembly, quality assessment and transcript quantification.
Brivez is a bioinformatic tool thought as Quality of Life's improvement, providing high quantity of data in a snap, giving you a quick view on what you could find inside your transcriptome/sequences' list.
Transcriptome analytic tools for non-model organism
Add a description, image, and links to the transcriptome topic page so that developers can more easily learn about it.
To associate your repository with the transcriptome topic, visit your repo's landing page and select "manage topics."