Pinned Repositories
10xPilot_snRNAseq-human
10x snRNA-seq study on 5 postmortem human brain regions across the reward circuitry: NAc, AMY, sACC, DLPFC, and HPC
cuRRBS
Simple and robust evaluation of enzyme combinations for reduced representation approaches
dev-kidney-snATAC
Codes used in the developmental kidney snATAC-seq data
md2pptx
Markdown To PowerPoint converter
phiclust
A clusterability measure for scRNA-seq data.
rmimp
Predicting the impact of mutations on kinase–substrate phosphorylation
RRBSsim
RRBSsim: reduced representation bisulfite sequencing simulator for next-generation sequencing
scatterpie
:art: scatter pie plot
SCEVAN
R package that automatically classifies the cells in the scRNA data by segregating non-malignant cells of tumor microenviroment from the malignant cells. It also infers the copy number profile of malignant cells, identifies subclonal structures and analyses the specific and shared alterations of each subpopulation.
spacexr
Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial transcriptomics
qindan2008's Repositories
qindan2008/arriba
Fast and accurate gene fusion detection from RNA-Seq data
qindan2008/AtacAnnoR
An accurate and robust cross-modality cell type annotation method for scATAC-seq data
qindan2008/cancereffectsizeR
cancereffectsizeR: an R package to measure the cancer effect size of somatic mutations
qindan2008/CC-Singlecell
A project focused on using single-cell RNA sequencing data (scRNA-seq) and pseudo time to improve colon cancer diagnosis and outcomes.
qindan2008/CellBender
CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
qindan2008/CellHeapRelease
qindan2008/Drug_Explorer
Interactive & explainable GNN for drug repurposing
qindan2008/dseqr
single-cell and bulk RNA-seq analyses from counts → pathways → drug candidates.
qindan2008/focal-amplification
qindan2008/kraken2
The second version of the Kraken taxonomic sequence classification system
qindan2008/LiverAnnotation
qindan2008/LiverMap2.0
qindan2008/MACA
MACA: Marker-based automatic cell-type annotation for single cell expression data
qindan2008/Onco-fetal-CAF-in-HCC
qindan2008/promor
A comprehensive R package for label-free proteomics data analysis and modeling
qindan2008/r-scan2
R package supporting the SCAN2 pipeline
qindan2008/richR
Function Enrichment analysis and Network construction
qindan2008/rnaseqc
Fast, efficient RNA-Seq metrics for quality control and process optimization
qindan2008/scAmpi_single_cell_RNA
Code related to scRNA analysis using the scAmpi workflow
qindan2008/SCAN2
SCAN2 is a somatic SNV and indel genotyper for single cells amplified by Primary Template-Directed Amplification (PTA)
qindan2008/scExtras
qindan2008/scMTNI
qindan2008/scRNA-seq_notes
A list of scRNA-seq analysis tools
qindan2008/scRNA_shiny
scRNA-seq Shiny App
qindan2008/scRNAseq-analysis-notes
scRNAseq analysis notes from Ming Tang
qindan2008/SCRuB_analysis
qindan2008/scsampler
qindan2008/scViewer
qindan2008/ShinyCell
Shiny Interactive Web Apps for Single-Cell Data
qindan2008/stLearn
A novel machine learning pipeline to analyse spatial transcriptomics data