Discover Oshlack/combes-organoid-paper Open Source project

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R
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MIT License
Created about 6 years ago
Updated almost 6 years ago

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Analysis code and output for the Combes kidney organoid scRNA-seq paper https://doi.org/10.1186/s13073-019-0615-0

splatter

Simple simulation of single-cell RNA sequencing data

204

JAFFA

JAFFA is a multi-step pipeline that takes either raw RNA-Seq reads, or pre-assembled transcripts, then searches for gene fusions

C++

Corset

Software for clustering de novo assembled transcripts and counting overlapping reads

C++

Lace

Building SuperTranscripts: A linear representation of transcriptome data

Python

STRetch

Method for detecting STR expansions from short-read sequencing data

Python

Clinker

Gene Fusion Visualiser

Python

speckle

R package for specialised analysis of single cell data

MINTIE

Method for Identifying Novel Transcripts and Isoforms using Equivalence classes, in cancer and rare disease.

Python

splatter-paper

Data and analysis for the Splatter paper

necklace

Combine reference and assembled transcriptomes for RNA-Seq analysis

C++

Slinker

Slinker offers a succinct and complementary method to visualise RNA-Seq data through superTranscripts.

Python

ALLSorts

ALLSorts is a B-Cell Acute Lymphoblastic Leukemia (B-ALL) subtype classifier. From gene expression counts to over 18 subtypes.

Python

MethylationAnalysisWorkflow

A cross-package Bioconductor workflow for analysing methylation array data

TeX

missMethyl

Bioconductor package for analysis of methylation data from Illumina's Infinium HumanMethylation arrays.

GeneLengthBias-scRNASeq

Analysis scripts for eight different scRNASeq datasets that differ in terms of protocol, species and cell type

superTranscript_paper_code

This repository contains code and scripts used to generate and analyse data for the superTranscript/Lace paper.

Jupyter Notebook

scRNAtools-paper

A review of tools for analysing single-cell RNA-seq data

TeX

methyl-geneset-testing

Toblerone

Rust

ec-dtu-pipe

Pipeline for performing differential transcript usage analysis using equivalence classes, transcript quantifications and/or exon counts

hashtag-demux-paper

Analysis code for "Benchmarking single-cell hashtag oligo demultiplexing methods" paper

paed-cf-cite-seq

OrganoidVarAnalysis

TALLSorts

Python

oshlack.github.io

Oshlack Lab website

JavaScript

ALL-RNAseq-utility-paper

Oncopipe

Clinical pipeline for detecting gene fusions in RNAseq data utilising JAFFA.

Groovy

Oshlack/combes-organoid-paper

Oshlack

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