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.
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Updated
Mar 20, 2018 - Python
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 pipeline to validate exfi's performance
Simulating RNA-Seq reads from transcriptome to test software (e.g. for Drop-Seq singleCell software)
A snakemake workflow for performing de novo transcriptome assembly, quality assessment and transcript quantification.
Get exons from a transcriptome and raw genomic reads using abyss-bloom and bedtools
SIMulator for Long read transcriptome Analysis with RNA DecaY model
Use scaffold realigning strategy to detect the recurrence of a list fusion transcripts across samples
Snakemake workflow to run transdecoder + trinotate
Derives consensus sequences from a set of long noisy reads by clustering and error correction.
De novo clustering of long transcript reads into genes
Blast wrapper using snakemake to generate correspondance between a list of transcript or protein and some proteomes.
Escherichia coli Transcriptome Assembly from a Compendium of RNA-seq Data Sets
Transcriptome analytic tools for non-model organism
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.
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).
de novo assembly of RNA-seq data using ABySS
Merging, Annotation, Validation, and Illustration of Structural variants
Demultiplexing and debarcoding tool designed for LR-Split-seq 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.
Technology agnostic long read analysis pipeline for transcriptomes
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