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
qindan2008/10xPilot_snRNAseq-human
10x snRNA-seq study on 5 postmortem human brain regions across the reward circuitry: NAc, AMY, sACC, DLPFC, and HPC
qindan2008/16S-vsearch-nf
vsearch based 16S targeted metagenomics pipeline
qindan2008/book-genekitr
📚 Book for Genekitr
qindan2008/CellphoneDB
CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
qindan2008/ChartFun
🎲 数据大屏可视化编辑器
qindan2008/COPILOT
Single cell RNA-seq preprocessing tool for gene-by-cell matrices of UMI counts. It is recommended to use the raw spliced and unpliced counts matrices produced by scKB pipeline as the input of copilot.
qindan2008/copykit
Toolkit for single-cell copy number analysis
qindan2008/datav-vue
A Powerful Data Visualization Tool. Uses TypeScript And Vue3. Scenario-specific templates. User-friendly interfaces. 一款数据可视化应用搭建工具
qindan2008/dropEst
Pipeline for initial analysis of droplet-based single-cell RNA-seq data
qindan2008/excelerate-scRNAseq
Single RNA-seq data analysis with R (Finland, May, 2019)
qindan2008/gEAR
The gEAR Portal was created as a data archive and viewer for gene expression data including microarrays, bulk RNA-Seq, single-cell RNA-Seq and more.
qindan2008/ggExpress
ggExpress is the fastest way to create, annotate and and save plots in R.
qindan2008/ggpmisc
R package ggpmisc is an extension to ggplot2 and the Grammar of Graphics
qindan2008/iobio-gru-backend
qindan2008/LiBis
qindan2008/muon-tutorials
Tutorials for multimodal omics data analysis
qindan2008/NeuralEE
NeuralEE: a GPU-accelerated elastic embedding dimensionality reduction Python package for visualization of large-scale scRNA-seq data.
qindan2008/OmnipathR
R client for the OmniPath web service
qindan2008/pixarfilms
:movie_camera: R data package to explore Pixar films, the people, and reception data
qindan2008/popsicleR
popsicleR, a flexible R package aimed at providing most of the necessary quality controls and preliminary information for complete and detailed analysis of single cell RNA-seq data.
qindan2008/scAnalyzer
Integrative analysis pipeline for scRNA-seq data
qindan2008/scGate.demo
qindan2008/scGeneFit-python
Python code for genetic marker selection using linear programming
qindan2008/scnym
Semi-supervised adversarial neural networks for classification of single cell transcriptomics data
qindan2008/scxa-workflows
Higher level repo for aggregating all of Atlas workflow logic for Single Cell
qindan2008/sspbc
Single-Sample Predictors for Breast Cancer (sspbc) include functions and models to assign classes to breast cancer samples using gene expression data.
qindan2008/STAR_Methods
This repository contains examples of code used to generate the figures in the manuscript: Human colorectal pre-cancer atlas identifies distinct molecular programs underlying two major subclasses of pre-malignant tumors
qindan2008/TREG
Tools for finding Total RNA Expression Genes in single nucleus RNA-seq data
qindan2008/ultraheatmap
extra pumped heatmaps
qindan2008/workflowr
Organize your project into a research website