semir2's repositories
2020_DeepIS
嵌合T细胞受体Code used for "Deep-learning based three-dimensional label-free tracking and analysis of immunological synapses of chimeric antigen receptor T cells"
2020_Wilk_COVID
新冠数据与代码Reproducibility repository accompanying Wilk, Rustagi, Zhao, et al. "A single-cell atlas of the peripheral immune response to severe COVID-19"
bookdown
R进行某些软件说明的写书的软件 Authoring Books and Technical Documents with R Markdown
cellSNP
Pileup biallelic SNPs from single-cell and bulk RNA-seq data
clustifyr
单细胞与普通bulk RNA数据的比对分析，会出热图，与seurat兼容Infer cell types in scRNA-seq data using bulk RNA-seq or gene sets
DeepCE
Code and Datasets for the paper "A deep learning framework for high-throughput mechanism-driven phenotype compound screening and its application to COVID-19 drug repurposing", published on Nature Machine Intelligence in 2021.
DISC
单细胞转录组数据填补的方法，中山大学谢老师A highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning.
DoubletDecon
A tool for removing doublets from single-cell RNA-seq data
Giotto
空间转录组工具Single-cell spatial analysis toolbox
ImmunogenomicLandscape-BloodCancers
2020年Cancer Cell研究绘制恶性血液病的免疫-基因组学图谱的脚本Scripts related to Dufva and Pölönen et al. Immunogenomic landscape of hematological malignancies project
kortekaas2020_paper
Single cell RNA-seq analysis accompanying Kortekaas, Santegoets et al. 10.1158/2326-6066.CIR-20-0270 doi: (2020)
MATHLA
A robust framework for HLA-peptide binding pre-diction integrating bidirectional LSTM and multiple head attention mechanism.
mixcr
MiXCR is a universal software for fast and accurate extraction of T- and B- cell receptor repertoires from any type of sequencing data. Free for academic use only.
MuSiC
单细胞免疫浸润工具-Multi-subject Single Cell Deconvolution
proteomesoflife
2020年nature100个物种蛋白组学谱系python based queries for the proteomesoflife neo4j network database
RapMap
快速比对的软件Rapid sensitive and accurate read mapping via quasi-mapping
scanorama
2019年发表在NB上的单细胞转录组批次校正的方法Panoramic stitching of single cell data
scCancer
单细胞转录组癌症分析流程整合A package for automated processing of single cell RNA-seq data in cancer
scCATCH_performance_comparison
单细胞自动化鉴定工具的评估The source code and results of performance comparison on the detail of the process among scCATCH, CellAssign, Garnett, SingleR, scMap and CHETAH, and CellMatch database
scg_lib_structs
Collections of library structure and sequence of popular single cell genomic methods
scRepertoire
单细胞VDJ工具A toolkit for single-cell immune profiling
scTE
单细胞转录组转座子工具
Sierra
转录本使用的分析Discover differential transcript usage from polyA-captured single cell RNA-seq data
singlecell_endodiff_paper
单细胞关于SNP文章相应的脚本Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression
tanaylab.github.io
单细胞转录组转座子
tenx
10xGenomics单细胞转录组官方和seurat流程串联起来了Pipelines for the analysis of 10x single-cell RNA-sequencing data
vcf2maf
Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
Viral-Track
单细胞转录组-宿主与病毒之间的互作工具