Eunchae Yeo's repositories
AmpliconClassifier
Classify output of AmpliconArchitect to detect types of focal amplifications present
trinityrnaseq
Trinity RNA-Seq de novo transcriptome assembly
bwa
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
CHM13
The complete sequence of a human genome
gatk
Official code repository for GATK versions 4 and up
learn-wdl
Educational materials for learning WDL
RSEM
RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
scCNAutils
Functions to analyze copy number aberrations in single-cell data
xCell
Cell types enrichment analysis
pyclone
Probabilistic model for inferring clonal population structure from deep NGS sequencing.
GLASS
GLASS consortium
ConsensusTME
ConsensusTME Gene Sets and R Script
gatk4-somatic-cnvs
This repo is archived, these workflows will be housed in the GATK repository under the scripts directory. These workflows are also organized in Dockstore in the GATK Best Practices Workflows collection.
gatk4-somatic-snvs-indels
This repo has been archived, these workflows are still available in the GATK repository under the scripts directory. The workflows are also organized in Dockstore in the GATK Best Practices Workflows collection.
MISO
MISO: Mixture of Isoforms model for RNA-Seq isoform quantitation
juncBASE
Junction Based Analysis of Splicing Events for RNA-Seq