| Biological samples |
|
| Surgically dissected human PDAC tissue |
This paper |
N/A |
|
| Critical commercial assays |
|
| Chromium Next GEM Single Cell 3′ Kit v3.1 |
10X Genomics |
Cat# PN-1000269 |
| Chromium Next GEM Chip G Single Cell Kit |
10X Genomics |
Cat# PN-1000127 |
| Dual Index Kit TT Set A |
10X Genomics |
Cat# PN-1000215 |
|
| Deposited data |
|
| PDAC scRNAseq (OUGS) |
This paper |
zenodo [10.5281/zenodo.6024273]
OUGS1 (60 year old male); OUGS2 (73 year old male); OUGS3 (74 year old female); OUGS4 (83 year old female). |
| PDAC scRNAseq (PRJCA001063) |
(Peng et al., 2019a) |
zenodo [10.5281/zenodo.3969339] |
| PDAC scRNAseq (GSE155698) |
(Steele et al., 2020) |
GEO: GSE155698
|
| PDAC scRNAseq (GSE111672) |
(Moncada et al., 2020) |
GEO: GSE111672
|
| PDAC scRNAseq (GSE154778) |
(Lin et al., 2020) |
GEO: GSE154778
|
| PDAC scRNAseq (GSM4293555) |
(Schlesinger et al., 2020) |
GEO: GSM4293555
|
| Upregulated gene list of TCGA-PAAD RNAseq |
(Tang et al., 2019) |
http://gepia2.cancer-pku.cn/#index |
PDAC bulk RNAseq
TCGA-PAAD |
Firehose |
https://gdac.broadinstitute.org/ |
PDAC bulk RNAseq
ICGA-PACA-AU |
ICGA |
https://dcc.icgc.org/releases/current/Projects/PAEN-AU |
PDAC bulk RNAseq
ICGA-PACA-CA |
ICGA |
https://dcc.icgc.org/releases/current/Projects/PACA-CA |
| PDAC bulk RNAseq |
(Dijk et al., 2020) |
ArrayExpress, E-MTAB-6830 |
PDAC genomic mutation file
TCGA-PAAD |
GDC via TCGAbiolinks |
https://portal.gdc.cancer.gov/ |
|
| Software and algorithms |
|
| R (v4.1.2) |
R CRAN |
https://cran.r-project.org/ |
| Seurat R package (v4.0.5) |
(Hao et al., 2021)
R CRAN |
https://cran.r-project.org/web/packages/Seurat/index.html |
| pheatmap R package (v1.0.12) |
R CRAN |
https://cran.r-project.org/web/packages/pheatmap/index.html |
| ComplexHeatmap R package (v2.10.0) |
Bioconductor |
https://www.bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html |
| ggplot2 R package (v3.3.5) |
R CRAN |
https://cran.r-project.org/web/packages/ggplot2/index.html |
| ktplots R package (v1.1.14) |
Github |
https://github.com/zktuong/ktplots
https://zenodo.org/record/5717923#.Ynyu31TP0SE
|
| survival R package (v3.2-13) |
R CRAN |
https://cran.r-project.org/web/packages/survival/index.html |
| ensembldb R package (v 2.18.1) |
Bioconductor |
https://bioconductor.org/packages/release/bioc/html/ensembldb.html |
| EnsDb.Hsapiens.v86 R package (v 2.99.0) |
Bioconductor |
http://bioconductor.org/packages/release/data/annotation/html/EnsDb.Hsapiens.v86.html |
| BisuqeRNA R package (v1.0.5) |
(Jew et al., 2020)
R CRAN |
https://cran.r-project.org/web/packages/BisqueRNA/index.html |
| TCGAbiolinks R package (v2.22.1) |
(Colaprico et al., 2016)
Bioconductor |
https://bioconductor.org/packages/release/bioc/html/TCGAbiolinks.html |
| CellChat R package (v1.1.3) |
(Jin et al., 2021)
Github |
https://github.com/sqjin/CellChat |
| SCENIC R package (v1.2.4) |
(Aibar et al., 2017)
Github |
https://github.com/aertslab/SCENIC |
| clusterProfilerR package (v4.2.0) |
(Wu et al., 2021)
Bioconductor |
https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html |
| ReactomePA R package (v1.38.0) |
(Yu and He, 2016)
Bioconductor |
https://bioconductor.org/packages/release/bioc/html/ReactomePA.html |
| DOSE R package (v3.20.0) |
(Yu et al., 2014)
Bioconductor |
https://bioconductor.org/packages/release/bioc/html/DOSE.html |
| enrichplot R package (v1.14.1) |
Bioconductor |
https://bioconductor.org/packages/release/bioc/html/enrichplot.html |
| org.Hs.eg.db R package (v3.14.0) |
Bioconductor |
https://bioconductor.org/packages/release/data/annotation/html/org.Hs.eg.db.html |
| AnnotationDbi R package (v1.56.1) |
Bioconductor |
https://bioconductor.org/packages/release/bioc/html/AnnotationDbi.html |
| nichenetr R package (v1.0.0) |
(Browaeys et al., 2020)
Github |
https://github.com/saeyslab/nichenetr |
| networkD3 R package (v0.4) |
CRAN |
https://cran.r-project.org/web/packages/networkD3/index.html |
| fastp v0.20.1 |
(Chen et al., 2018) |
https://github.com/OpenGene/fastp |
| STAR v2.7.9a |
(Dobin et al., 2013) |
https://github.com/alexdobin/STAR |
| RSEM v1.3.3 |
(Li and Dewey, 2011) |
https://github.com/deweylab/RSEM |
