SpaceFold_paper

Default Boolean Operator: Terms in a search string will be connected by the AND operator, EXAMPLE: searching genomic melanoma will produce the same results as genomic AND melanoma .
AND, OR, NOT: Combine terms in a search with the boolean operators AND (to add specificity), OR (to broaden), or NOT (to eliminate a term). Operators must be capitalized (all other search terms are not case-sensitive).
Wild Card: Add wild card symbols * (open-ended) and ? (single character) to truncate terms. EXAMPLE: searching gen* shows results for 'gene', 'genetic', 'genomic, etc. Searching gene? returns results for 'gene' or 'genes' but not for 'genome'.
Phrase Searching: Enclose search in quotation marks "keyword or search term" to search for an exact phrase. EXAMPLE: "transcription factors" returns results for records where transcription is immediately followed by the word factors .
Diacritics: Words containing diacritics translate those characters to non-diacritic form. EXAMPLE: massague returns results for Massague&#769 .
Filter by: Located on the homepage (left panel), use filters to search for records or narrow the search. From search results page, filters can be removed by clicking on the term at the top of the page.

UID: 11342

Author(s): Chu, Tin Yi* * MSK affiliated

Description: Description from GitHub:

"Space Ranger output and the h5ad files of the scRNA-seq data can be downloaded from https://doi.org/10.6084/m9.figshare.19715029 ."

Description from figshare:

"jupyter notebooks and R code and dataset related to the SpaceFold paper."

Subject(s)

Access via GitHub

Access via figshare
Access Restrictions: Free to All
Access Instructions: Available for download via a CC by 4.0 license
Associated Publications: Niec R, Chu T, Schernthanner M, Gur-Cohen S, Hidalgo L, Pasolli H, Luckett K, Wang Z, Bhalla S, Cambuli F, Kataru R, Ganesh K, Mehrara B, Pe'er D, Fuchs E. Lymphatics act as a signaling hub to regulate intestinal stem cell activity. Cell Stem Cell. 2022; 29(7):1067-1082.e18.
Software Used: BayesPrism
Bayesian cell Proportion Reconstruction Inferred using Statistical Marginalization (BayesPrism): A Fully Bayesian Inference of Tumor Microenvironment composition and gene expression

R
a free software environment for statistical computing and graphics.

Space Ranger
Dataset Format(s): R, PDF, TSV, H5AD, zip, IPYNB
Dataset Size: 5.57 GB

Do you have or know of a dataset that should be added to the catalog? Let us know!