Oshlack/ec-dtu-pipe Oshlack/ec-dtu-pipe

  • Stars
    star
    4
  • Rank 3,304,323 (Top 66 %)
  • Language
    R
  • License
    MIT License
  • Created almost 6 years ago
  • Updated over 4 years ago
Twitter logo Share LinkedIn logo Share Facebook logo Share
Oshlack/ec-dtu-pipe
github

Oshlack

Reviews

There are no reviews yet. Be the first to send feedback to the community and the maintainers!

Repository Details

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

More Repositories

1

splatter

Simple simulation of single-cell RNA sequencing data
R
204
star
2

JAFFA

JAFFA is a multi-step pipeline that takes either raw RNA-Seq reads, or pre-assembled transcripts, then searches for gene fusions
C++
74
star
3

Corset

Software for clustering de novo assembled transcripts and counting overlapping reads
C++
67
star
4

Lace

Building SuperTranscripts: A linear representation of transcriptome data
Python
67
star
5

STRetch

Method for detecting STR expansions from short-read sequencing data
Python
62
star
6

Clinker

Gene Fusion Visualiser
Python
49
star
7

speckle

R package for specialised analysis of single cell data
R
34
star
8

MINTIE

Method for Identifying Novel Transcripts and Isoforms using Equivalence classes, in cancer and rare disease.
Python
33
star
9

splatter-paper

Data and analysis for the Splatter paper
R
27
star
10

necklace

Combine reference and assembled transcriptomes for RNA-Seq analysis
C++
21
star
11

Slinker

Slinker offers a succinct and complementary method to visualise RNA-Seq data through superTranscripts.
Python
18
star
12

ALLSorts

ALLSorts is a B-Cell Acute Lymphoblastic Leukemia (B-ALL) subtype classifier. From gene expression counts to over 18 subtypes.
Python
15
star
13

MethylationAnalysisWorkflow

A cross-package Bioconductor workflow for analysing methylation array data
TeX
11
star
14

missMethyl

Bioconductor package for analysis of methylation data from Illumina's Infinium HumanMethylation arrays.
R
10
star
15

GeneLengthBias-scRNASeq

Analysis scripts for eight different scRNASeq datasets that differ in terms of protocol, species and cell type
9
star
16

superTranscript_paper_code

This repository contains code and scripts used to generate and analyse data for the superTranscript/Lace paper.
Jupyter Notebook
9
star
17

combes-organoid-paper

Analysis code and output for the Combes kidney organoid scRNA-seq paper https://doi.org/10.1186/s13073-019-0615-0
R
6
star
18

scRNAtools-paper

A review of tools for analysing single-cell RNA-seq data
TeX
5
star
19

methyl-geneset-testing

R
5
star
20

Toblerone

Rust
4
star
21

hashtag-demux-paper

Analysis code for "Benchmarking single-cell hashtag oligo demultiplexing methods" paper
R
3
star
22

paed-cf-cite-seq

R
2
star
23

OrganoidVarAnalysis

R
2
star
24

TALLSorts

Python
2
star
25

oshlack.github.io

Oshlack Lab website
JavaScript
2
star
26

ALL-RNAseq-utility-paper

R
2
star
27

Oncopipe

Clinical pipeline for detecting gene fusions in RNAseq data utilising JAFFA.
Groovy
1
star