| Deposited data |
|
| GSE143607 |
New dataset |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE143607 |
| E-MTAB-2600 |
ArrayExpress |
https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-2600/ |
| E-MTAB-2805 |
ArrayExpress |
https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-2805/ |
| E-MTAB-2512 |
ArrayExpress |
https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-2512 |
| E-MTAB-3857 |
ArrayExpress |
https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3857 |
| E-MTAB-4619 |
ArrayExpress |
https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-4619 |
| E-MTAB-3929 |
ArrayExpress |
https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3929 |
| PBMCs from a Healthy Donor: Whole Transcriptome Analysis (v3.1 chemisty) |
10xGenomics |
https://support.10xgenomics.com/single-cell-gene-expression/datasets |
| Hodgkin's Lymphoma, Dissociated Tumor: Whole Transcriptome Analysis (v3.1 chemisty) |
10xGenomics |
https://support.10xgenomics.com/single-cell-gene-expression/datasets |
| 1k Brain Nuclei from an E18 Mouse (v2 chemistry) |
10xGenomics |
https://support.10xgenomics.com/single-cell-gene-expression/datasets |
| Pan T Cells isolated from mononuclear cells of a healthy donor |
10xGenomics |
https://www.10xgenomics.com/resources/datasets/4-k-pan-t-cells-from-a-healthy-donor-2-standard-2-1-0 |
| 1k PBMCs from a Healthy Donor (v3 chemistry) |
10xGenomics |
https://support.10xgenomics.com/single-cell-gene-expression/datasets |
| PRJDB5282 |
DDBJ |
https://ddbj.nig.ac.jp/BPSearch/bioproject?acc=PRJDB5282 |
| PRJEB8994 |
ENA |
https://www.ebi.ac.uk/ena/browser/view/PRJEB8994 |
| GSE42268 |
NCBI GEO |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42268 |
| GSE53386 |
NCBI GEO |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53386 |
| GSE98664 |
NCBI GEO |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE98664 |
| GSE74833 |
NCBI GEO |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE74833 |
| GSE67310 |
NCBI GEO |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE67310 |
| GSE45719 |
NCBI GEO |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45719 |
| GSE75659 |
NCBI GEO |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE75659 |
| GSE59114 |
NCBI GEO |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59114 |
| GSE68981 |
NCBI GEO |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE68981 |
| GSE70657 |
NCBI GEO |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70657 |
| GSE56638 |
NCBI GEO |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE56638 |
| GSE64016 |
NCBI GEO |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE64016 |
| GSE75748 |
NCBI GEO |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE75748 |
| GSE70151 |
NCBI GEO |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70151 |
| GSE29087 |
NCBI GEO |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29087 |
| GSE46980 |
NCBI GEO |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE46980 |
| GSE54695 |
NCBI GEO |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE54695 |
| GSE78779 |
NCBI GEO |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE78779 |
|
| Experimental models: cell lines |
|
| MCF10A |
ATCC |
CRL-10317 |
|
| Software and algorithms |
|
| NCBI Entrez Programming Utilities |
NCBI |
https://www.ncbi.nlm.nih.gov/books/NBK25501/ |
| Bioconductor |
(Gentleman et al., 2004) |
https://www.bioconductor.org/ |
| DESeq2 |
(Love et al., 2014) |
http://bioconductor.org/packages/release/http://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| Python |
Python programming language |
https://www.python.org/ |
| ImageJ |
NIH |
https://imagej.nih.gov/ij/ |
| Seurat |
https://doi.org/10.1016/j.cell.2019.05.031 |
https://satijalab.org/seurat/ |
