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ALLSorts is a B-Cell Acute Lymphoblastic Leukemia (B-ALL) subtype classifier. From gene expression counts to over 18 subtypes.
An Acute Lymphoblasitc Leukemia B-Cell classifier
Code for generating the figures and analyses presented in the MINTIE paper
JAFFA is a multi-step pipeline that takes either raw RNA-Seq reads, or pre-assembled transcripts, then searches for gene fusions
A method for identifying transcriptional variants in cancer and rare disease
R package for the compositional analysis of single cell data
Bioconductor package for analysis of methylation data from Illumina's Infinium HumanMethylation arrays.
Simple simulation of single-cell RNA sequencing data
Oshlack Lab website
Method for detecting STR expansions from short-read sequencing data
Combine reference and assembled transcriptomes for RNA-Seq analysis
Building SuperTranscripts: A linear representation of transcriptome data
Fast and accurate differential transcript usage by testing equivalence class counts
Pipeline for performing differential transcript usage analysis using equivalence classes, transcript quantifications and/or exon counts
Gene Fusion Visualiser
Software for clustering de novo assembled transcripts and counting overlapping reads
Code and analysis for the pooled parents paper
Basic bpipe pipeline stages and pipelines for RNA/DNAseq analysis.
Analysis code and output for the Combes kidney organoid scRNA-seq paper
A review of tools for analysing single-cell RNA-seq data
Paper describing the clustering tree visualisation
Data and analysis for the Splatter paper
Clinical pipeline for detecting gene fusions in RNAseq data utilising JAFFA.
This repository contains code and scripts used to generate and analyse data for the superTranscript/Lace paper.
This repository contains code from the paper Farlie et al.
A cross-package Bioconductor workflow for analysing methylation array data
Analysis scripts for eight different scRNASeq datasets that differ in terms of protocol, species and cell type