Pinned Repositories
ASE_Central
A repo whose main purpose is to point to the many repos we created for our ASE project
ASE_pipeline
Our basic allele specific analysis pipeline for single nuclei data, based on nextflow
BulkIsoform
Upstream pipeline for bulk RNASeq preprocessing and R package for downstream analysis
CellLevel_QC
A simple java based command to extract QC information (%intronic, %antisense, etc) from a CellRanger bam file.
CellTypeComp
Test different methods for cell type composition analysis
CompareSequence
Code used to compare sequencing techs
ivPerturbSeq
Code for in vivo Perturb-seq
PrivMCMC
PrivSTRAT
scAlleleExpression
An R package for SNP level allelic expression analysis of single cell or nuclei data.
seanken's Repositories
seanken/CellLevel_QC
A simple java based command to extract QC information (%intronic, %antisense, etc) from a CellRanger bam file.
seanken/CompareSequence
Code used to compare sequencing techs
seanken/CellTypeComp
Test different methods for cell type composition analysis
seanken/ivPerturbSeq
Code for in vivo Perturb-seq
seanken/PrivMCMC
seanken/PrivSTRAT
seanken/ASE_Central
A repo whose main purpose is to point to the many repos we created for our ASE project
seanken/ASE_pipeline
Our basic allele specific analysis pipeline for single nuclei data, based on nextflow
seanken/DP_count
Privacy Preserving Medical Count Queries
seanken/FivePrime
Code for our fiveprime RNASeq project
seanken/scAlleleExpression
An R package for SNP level allelic expression analysis of single cell or nuclei data.
seanken/BulkIsoform
Upstream pipeline for bulk RNASeq preprocessing and R package for downstream analysis
seanken/AllelicTest
Code for Allelic test statistic
seanken/ASE_LongRead
A pipeline to get gene and isoform level ASE information from long read data.
seanken/ASE_Plots
Code for plots for ASE paper
seanken/LogAttack
seanken/LupusModel
seanken/sc_compare_helpers
seanken/scASE_py
Python directory to process the output of our ASE pipeline
seanken/SciFi_Pipeline
seanken/seanken.github.io
seanken/seurat
R toolkit for single cell genomics
seanken/SimpleBlog
seanken/SingleCellPackage
Some basic tools used in many single cell analysis
seanken/UsingSierra
Scripts to use Sierra