Pipeline for low-level RNA-Seq data processing
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Updated
Oct 4, 2016 - R
Pipeline for low-level RNA-Seq data processing
A utility to call polyA sites based on genome alignments in SAM format
Comparing 3' single-end sequencing for genome and txome
Back-end R package for running anexvis web application
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.
Massively Parallel RNA-seq Project
The package RNAseqAnalysis does the complete analysis of RNA seq data starting from raw reads. It provides the user with differnt functions like generation of qc report, filtering, assembly and GO-term annotation, differential expression analysis and heatmap generation, and Alternative splicing-site prediction
Deconvolution of transcriptome through Immune Component Analysis
Snakemake pipeline to validate exfi's performance
Virusfishing is a virus screening pipeline for 1000 Insect Transcriptome Evolution (1KITE) project to search viruses, construct viral genomes and screen for the expressed virus genes and discover viral splicing patterns. Virusfishing also can be used in other next generation sequencing data.
Automated Isoform Discovery Detector (AIDD)
Building classifiers using cancer transcriptomes across 33 different cancer-types
De nove assembly and annotation of Fragilaria radians transcriptome
AnceTran2.0: R package for transcriptome evolution analysis based on RNA-seq expression data or ChIP-seq TF-binding data
Polytranscript risk scoring (PTRS)
Code to model distribution of transcript abundances.
TreeExp 2.0: Toolbox for analyzing expression evolution based on RNA-seq count data
Splice-aware Tool for Alignment of Pyrosequencing Reads
Simulating RNA-Seq reads from transcriptome to test software (e.g. for Drop-Seq singleCell software)
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