Table 1.
Dataset overview. Datasets include hematopoietic cells of peripheral blood and bone marrow, intestine and pancreas in health and disease. Besca’s functionality is exemplified on these datasets utilizing Jupyter notebooks (N), R markdowns (R), this manuscript (M) and its supplementals (S)
| Tissue | Area of interest | Dataset | Original data accession | Processed data DOI | CITE-seq | Standard workflow | Sig-annot, signature-based cell annotation | Auto-annot, supervised cell annotation | Bescape, bulk RNA-seq deconvolution |
|---|---|---|---|---|---|---|---|---|---|
| Bone marrow and peripheral blood | Healthy | PBMC3k | 10xgenomics.com | 10.5281/zenodo.3948150 | No | S, N | N | M4, S, N | - |
|
|
Mixed-phenotype acute leukemia | Granja2019 | GSE139369 | 10.5281/zenodo.3944753 | Yes | N | M2, N | M4, S, N | - |
|
|
Vaccine responsivenes | Kotliarov2020 | 10.35092/yhjc.c.4753772 | 10.5281/zenodo.3938290 | Yes | N | M3, N | M4, S, N | M6, R |
| Intestine | Ulcerative colitis | Smillie2019 | SCP259 | 10.5281/zenodo.3960617 | No | N | N | M5, S, N | - |
|
|
Crohn's disease | Martin2019 | GSE134809 | 10.5281/zenodo.3862132 | No | N | N | M5, S, N | - |
|
|
Mouse | Haber2017 | GSE92332 | 10.5281/zenodo.3935782 | No | N | N | M5, S, N | - |
|
|
Colorectal cancer | Lee2020 | GSE132465 | 10.5281/zenodo.3967538 | No | N | S, N | - | - |
| Pancreas | Type II Diabetes | Segerstolpe2016 | E-MTAB-5061 | 10.5281/zenodo.3928276 | No | N | N | S, N | M6, R |
|
|
Pancreatic ductal adenocarcinoma | Peng2019 | PRJCA001063 | 10.5281/zenodo.3969339 | No | N | S, N | S, N | - |
|
|
Healthy | Baron2016 | GSE84133 | 10.5281/zenodo.3968315 | No | N | N | S, N | - |
M = main manuscript; S = supplementary material; N = notebook on GitHub (https://github.com/bedapub/besca_publication_results); R = R Markdown on GitHub (https://github.com/bedapub/bescape)
2, Fig.2; 3, Fig. 3; 4, Fig. 4; 5, Fig. 5; 6, Fig. 6.