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
Back-end R package for running anexvis web application
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
Automated Isoform Discovery Detector (AIDD)
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)
TreeExp 2.0: Toolbox for analyzing expression evolution based on RNA-seq count data
A collection of custom scripts used in the placenta transcriptome paper, Gong et al. Nat Comm, 2021
RepeatMasker Trinity based Parse Script
This repository houses the pipeline I coded to perform differential analysis of transcriptomes from two oyster species, C. gigas and C. virginica and isolate genes in the apoptosis pathway.
Code to reproduce Adaptive elastic-net sparse PCA for robust cross-species, cross-platform analysis of complex gene expression data in Alzheimer’s disease (Hin et al.)
Shiny app that recopilates all gene expression of zebra fish and informs about the tissue and developmental stage in which the gene is expressed.
RefEx: a reference gene expression dataset of mammalian tissues and cell lines measured by different methods
Matrix factorization-based biological discovery from large-scale transcriptome data using easyMF
Code and example data for transcriptional-data-guided brain network classification
Role of CXCL9/10/11, CXCL13 and XCL1 in recruitment and suppression of cytotoxic T cells in renal cell carcinoma
Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
metabolic pathway modeling based on gene expression
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