sc_gout

scripts of article

cellranger

we analysis 10x Genomics data with cellranger v3.1.0 and 6.0.2

SampleID	NovaSeq-batch	GROUP	CellRangerVersion
Case01	20200609	Acute	3.1.0
Case02	20200609	Acute	3.1.0
Case03	20200609	Acute	3.1.0
Case04	20200609	Acute	3.1.0
Case05	20200609	Acute	3.1.0
Case06	20200609	Acute	3.1.0
Case07	20200609	Acute	3.1.0
YB	20200609	Health	3.1.0
N01F	20200915	Health	3.1.0
N05S	20201112	Health	3.1.0
Gout146	20210708	Synovial fluid	6.0.2
MH	20211103	Health	6.0.2
RG	20211103	Health	6.0.2
Gout151	20211103	Synovial fluid	6.0.2
Gout183	20211103	Synovial fluid	6.0.2

cell qc

we remain cells follow:

PBMC: (pc30m2h5_cell.qc.R, Gout_10x_detect_doublets.ipynb, and N01F_N05S_10x_detect_doublets.ipynb)

SF: SF_1_cell_qc.R

1. nFeature_RNA > 500
2. nFeature_RNA < 4500
3. percent.mt < 15
4. nCount_RNA < 30000
5. not doublets

SCT and rPCA integration (test PC30 and selecting PC50)

PBMC: pc30m2h5_cell.qc.R

SF: SF_1_cell_qc.R

selecting health controls as reference

Annotation main cell type by SingleR

1_PBMC_SYN_re_annot.R

Abundance test

0_paper_Fig01.R

A0_paper_Fig02-alt.R

subclustering

3_MainDEG.R

3_add_subclustering_DEG_Func.R

A0_paper_Fig03.R

IS and ES

A0_paper_Fig05_SCORE.R

CCI

0_paper_Fig06_CCI_PBMCacute.R

0_paper_FigCCI_combinePlot.R