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in-depth-ngs-data-analysis-course

RNA与Chip-seq联合分析Materials for 12-day course on analyzing RNA-Seq, ChIP-Seq and variant calling data.

infercnv

10xGenomic单细胞转录组cnv Inferring CNV from Single-Cell RNA-Seq

intarna

细菌的RNA之间的相互作用Efficient target prediction incorporating accessibility of interaction sites

iobr

IOBR is an R package to perform comprehensive analysis of tumor microenvironment and signatures for immuno-oncology.

isoseq-browser

三代转录组的可视化工具

ispn

italk

cell-cell communication之前通信，主要是与肿瘤相关

kallistobustools

单细胞数据处理工具，可以考虑多重比对，最大似然法进行reads分配kallisto | bustools workflow for pre-processing single-cell RNA-seq data

karyoploter

比较好看的基因在染色体上面的图karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome

kbet

单细胞转录组批次校正技术An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.

kidney_sc_immune

Repository for scRNAseq study of human kidneys

kortekaas2020_paper

Single cell RNA-seq analysis accompanying Kortekaas, Santegoets et al. 10.1158/2326-6066.CIR-20-0270 doi: (2020)

l1000fwd

药物与基因表达数据库Large-scale visualization of drug-induced transcriptomic signatures

l1kprocs

L1Procs is a parallel R package for L1000 data processing and analyzing. Major function of L1KProcs includes (a) l1kpreprocs, which preprocesses raw data, and generates normalized gene expression data; (b) egem, which provides some interesting genes as target related genes, and potential transcription factors involved in the function of the compounds; (c) csNMF, which can detect compound signatures, and provide interesting compounds as drug candidates.

ldsc

LD Score Regression (LDSC)

liger

多样品、多物种、多组学整合分析R package for integrating and analyzing multiple single-cell datasets

lincs

Library of Integrated Cellular Signatures L1000

lincs-cell-painting

Processed Cell Painting Data for the LINCS Drug Repurposing Project

lincs_moa_pred_implementation

ML classifiers used to predict Mechanism of Action of chemical perturbagens using L1000 gene expression data

maestro

Single-cell Transcriptome and Regulome Analysis Pipeline

manual-for-running-idp-pipeline

2+3可变剪切IDP pipeline for identifying novel genes and isoforms

manuscript-rep-phad

Scripts to process 10X BCR data and create an AIRR input file (to upload into RepSeq platform)

mapcloud

10X/SS2/spatial transcriptomics/genotyping internal cloud pipeline

mars

发现新的细胞类型以及细胞注释新工具Discovering novel cell types across heterogenous single-cell experiments

mathla

A robust framework for HLA-peptide binding pre-diction integrating bidirectional LSTM and multiple head attention mechanism.

mechanism-of-action-prediction

Deep learning system to predict drug mechanism of action from gene expression (L1000) and cell viability (PRISM) data

mem-examples

Marker Enrichment Modeling (MEM)

metaneighbor

细胞亚群之间的比较、质控工具 A method to rapidly assess cell type identity using both functional and random gene sets

methylmix

Identification of differentially methylated genes in biomedical data

migmap

HTS-compatible wrapper for IgBlast V-(D)-J mapping tool