Analysis pipelines for genomic sequencing data

🚦 Run Picard on BAM files and collate 90 metrics into one file.

Digital Expression Explorer 2 (DEE2): a repository of uniformly processed RNA-seq data

A comprehensive pipeline for RNAseq data analysis

RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.

Nature Medicine paper. A Multidimensional Precision Medicine Approach for Autism Subtype Identification.

A comprehensive pipeline for Ribo-seq data analysis

RNA-seq analyses.

Cluster-specific pseudo-bulk analysis of 10X single-cell RNA-seq data by connecting Seurat to the VBC RNA-seq pipeline.

RNA-Seq Analysis Workflow Generator

Preprocessing and differential expression analysis for QuantSeq 3' mRNA-seq data

ChiP-seq and DNase-seq ,Bulk RNA-seq,scRNA-seq processing pipeline via R and shell

Construction of IHGV sequences from RNA-seq

🩺 Assessing StringTie, Salmon, and Kallisto with simulated RNA-Seq reads with noises introduced in read- and annotation-level.

This project consists of various scripts that were used for analysis of RNA-Seq data. The scripts are not customised but basal level which one can use to fit into their suitable experimental design post modifications.

A single-cell multimodal omics method for simultaneously detecting chromatin architecture and mRNA expression by sequencing (scCARE-seq)

Data and code for RNA-seq analysis workshop in R

Tool to identify chimeric events from RNA-Seq data

Identification of novel lncRNAs in non-small cell lung cancer. RNA-sequencing course (467713), University of Bern