Nanopore sequence read simulator
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Updated
Mar 4, 2024 - Python
Nanopore sequence read simulator
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/
Technology agnostic long read analysis pipeline for transcriptomes
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.
Demultiplexing and debarcoding tool designed for LR-Split-seq data.
Merging, Annotation, Validation, and Illustration of Structural variants
de novo assembly of RNA-seq data using ABySS
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).
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
Escherichia coli Transcriptome Assembly from a Compendium of RNA-seq Data Sets
Blast wrapper using snakemake to generate correspondance between a list of transcript or protein and some proteomes.
De novo clustering of long transcript reads into genes
Derives consensus sequences from a set of long noisy reads by clustering and error correction.
Snakemake workflow to run transdecoder + trinotate
Use scaffold realigning strategy to detect the recurrence of a list fusion transcripts across samples
SIMulator for Long read transcriptome Analysis with RNA DecaY model
Get exons from a transcriptome and raw genomic reads using abyss-bloom and bedtools
A snakemake workflow for performing de novo transcriptome assembly, quality assessment and transcript quantification.
Simulating RNA-Seq reads from transcriptome to test software (e.g. for Drop-Seq singleCell software)
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