Oshlack

Pinned Repositories

Clinker
Gene Fusion Visualiser
Language:Python50 7 2912
Corset
Software for clustering de novo assembled transcripts and counting overlapping reads
Language:C++67 8 2018
JAFFA
JAFFA is a multi-step pipeline that takes either raw RNA-Seq reads, or pre-assembled transcripts, then searches for gene fusions
Language:C++77 5 9320
Lace
Building SuperTranscripts: A linear representation of transcriptome data
Language:Python66 11 3819
MINTIE
Method for Identifying Novel Transcripts and Isoforms using Equivalence classes, in cancer and rare disease.
Language:Python33 7 367
necklace
Combine reference and assembled transcriptomes for RNA-Seq analysis
Language:C++21 4 185
speckle
R package for specialised analysis of single cell data
Language:R34 11 115
splatter
Simple simulation of single-cell RNA sequencing data
Language:R209 6 14855
splatter-paper
Data and analysis for the Splatter paper
Language:R27 2 013
STRetch
Method for detecting STR expansions from short-read sequencing data
Language:Python61 7 3816

Oshlack's Repositories

Oshlack/splatter
Simple simulation of single-cell RNA sequencing data
Language:R209 6 14855
Oshlack/JAFFA
JAFFA is a multi-step pipeline that takes either raw RNA-Seq reads, or pre-assembled transcripts, then searches for gene fusions
Language:C++77 5 9320
Oshlack/Corset
Software for clustering de novo assembled transcripts and counting overlapping reads
Language:C++67 8 2018
Oshlack/Lace
Building SuperTranscripts: A linear representation of transcriptome data
Language:Python66 11 3819
Oshlack/STRetch
Method for detecting STR expansions from short-read sequencing data
Language:Python61 7 3816
Oshlack/Clinker
Gene Fusion Visualiser
Language:Python50 7 2912
Oshlack/speckle
R package for specialised analysis of single cell data
Language:R34 11 115
Oshlack/MINTIE
Method for Identifying Novel Transcripts and Isoforms using Equivalence classes, in cancer and rare disease.
Language:Python33 7 367
Oshlack/necklace
Combine reference and assembled transcriptomes for RNA-Seq analysis
Language:C++21 4 185
Oshlack/Slinker
Slinker offers a succinct and complementary method to visualise RNA-Seq data through superTranscripts.
Language:Python18 9 84
Oshlack/ALLSorts
ALLSorts is a B-Cell Acute Lymphoblastic Leukemia (B-ALL) subtype classifier. From gene expression counts to over 18 subtypes.
Language:Python15 8 137
Oshlack/missMethyl
Bioconductor package for analysis of methylation data from Illumina's Infinium HumanMethylation arrays.
Language:R9 2 164
Oshlack/combes-organoid-paper
Analysis code and output for the Combes kidney organoid scRNA-seq paper https://doi.org/10.1186/s13073-019-0615-0
Language:R7 8 12
Oshlack/methyl-geneset-testing
Language:R6 2 23
Oshlack/ec-dtu-pipe
Pipeline for performing differential transcript usage analysis using equivalence classes, transcript quantifications and/or exon counts
Language:R4 10 11
Oshlack/hashtag-demux-paper
Analysis code for "Benchmarking single-cell hashtag oligo demultiplexing methods" paper
Language:R3 8 0
Oshlack/Toblerone
Language:Rust3 2 21
Oshlack/ALL-RNAseq-utility-paper
Language:R2 2 0
Oshlack/OrganoidVarAnalysis
Language:R2 9 03
Oshlack/oshlack.github.io
Oshlack Lab website
Language:JavaScript2 3 05
Oshlack/paed-cf-cite-seq
Language:R2 8 10
Oshlack/TALLSorts
Language:Python2 9 50
Oshlack/AllSorts_v1
An Acute Lymphoblasitc Leukemia B-Cell classifier
Language:R0 6 02
Oshlack/TobleroneApp
Desktop app incorporating https://github.com/oshlack/toblerone
Language:JavaScript0 6 00
Oshlack/Damsel
Language:R9 0
Oshlack/ec-dtu-paper
Fast and accurate differential transcript usage by testing equivalence class counts
Language:R8 01
Oshlack/MINTIE-paper-analysis
Code for generating the figures and analyses presented in the MINTIE paper
Language:R9 01
Oshlack/pooled-parents-paper
Code and analysis for the pooled parents paper
Language:Python6 0
Oshlack/TopDeck
Language:HTML8 0
Oshlack/xenanoseq
Nanopore demultiplexing, QC and alignment pipeline for xenograph RNA-seq experiments
Language:Nextflow0 0