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sc_gout's Introduction

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

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