Python library to access Gene Expression Omnibus Database (GEO)

Detection of RNA modifications from Oxford Nanopore direct RNA sequencing reads (Liu*, Begik* et al., Nature Comm 2019)

Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.

A comprehensive pipeline for RNAseq data analysis

A pipeline to assess the quantification of transcripts.

DInoPORE: Direct detection of INOsines in native RNA with nanoPORE sequencing

R package for visualization and exploratory analysis of Oxford Nanopore direct RNA seq based polyA predictions

discovering novel biomarkers in RNA-Seq data with tree-based models and survival analysis

Constructing Neoantigen Vaccine Pipeline with pVACtools

An R package for finding non-adenosine residues in poly(A) tails of ONT direct RNA sequencing reads

Gene Set Enrichment Class Analysis for heterogeneous RNA sequencing data

Accurate and robust inference of genetic ancestry from cancer-derived molecular data across genomic platforms

As part of an overall strategy for improving therapies for childhood cancers, the PPTC seeks to develop models for the types of tumors that will be encountered in early phase clinical testing by establishing patient derived xenografts (PDXs) from high-risk childhood cancers refractory to current standard of care treatments. Genomic profiling of …

Annotation and Analysis of Deep Sequencing Variants from CirSeq

A collection of source codes for network-based multi-omics analysis using integrated genome-wide association studies (GWAS) and transcriptomic data to identify genetic contribution into lithium response in patients with bipolar disorder (BD).

This repository houses the Genomic Sequence Comparison Code (GSCC), a collection of Python scripts designed for genomic sequence analysis. Whether you're comparing suspected sequences with known reference sequences or delving into bioinformatics, GSCC provides versatile tools for pairwise alignment. Feel free to explore!

Python based script which enables you to translate DNA or RNA, targeted towards high school biology. U=A G=C and exc.

QUAlity control for RNA_Seq, a nextflow pipeline

RNA-Seq data analysis: whole transcriptome, stranded, dUTP method

Performed a differential gene expression analysis with RNA-seq that compares the expression in human control breast cancer cell lines with lines treated by silencing the NRDE2 gene. A Salmon + tximport + DESeq2 workflow was conducted to pursue this.