Package: cellOrigins 0.1.3
cellOrigins: Finds RNASeq Source Tissues Using In Situ Hybridisation Data
Finds the most likely originating tissue(s) and developmental stage(s) of tissue-specific RNA sequencing data. The package identifies both pure transcriptomes and mixtures of transcriptomes. The most likely identity is found through comparisons of the sequencing data with high-throughput in situ hybridisation patterns. Typical uses are the identification of cancer cell origins, validation of cell culture strain identities, validation of single-cell transcriptomes, and validation of identity and purity of flow-sorting and dissection sequencing products.
Authors:
cellOrigins_0.1.3.tar.gz
cellOrigins_0.1.3.zip(r-4.5)cellOrigins_0.1.3.zip(r-4.4)cellOrigins_0.1.3.zip(r-4.3)
cellOrigins_0.1.3.tgz(r-4.4-any)cellOrigins_0.1.3.tgz(r-4.3-any)
cellOrigins_0.1.3.tar.gz(r-4.5-noble)cellOrigins_0.1.3.tar.gz(r-4.4-noble)
cellOrigins_0.1.3.tgz(r-4.4-emscripten)cellOrigins_0.1.3.tgz(r-4.3-emscripten)
cellOrigins.pdf |cellOrigins.html✨
cellOrigins/json (API)
| # Install 'cellOrigins' in R: |
| install.packages('cellOrigins', repos = c('https://davidhmolnar.r-universe.dev', 'https://cloud.r-project.org')) |
- BDGP_insitu_dmel_embryo - Patterns of gene expression in Drosophila melanogaster embryos
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 4 years agofrom:13b80ca5a5. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 24 2024 |
| R-4.5-win | OK | Aug 24 2024 |
| R-4.5-linux | OK | Aug 24 2024 |
| R-4.4-win | OK | Aug 24 2024 |
| R-4.4-mac | OK | Aug 24 2024 |
| R-4.3-win | OK | Aug 24 2024 |
| R-4.3-mac | OK | Aug 24 2024 |
Exports:diagnosticPlotsdiagnosticPlots.listdiagnosticPlots.matrixdiscovery_probabilitydiscovery.identicdiscovery.lineardiscovery.logiterating_seqVsInsituprior.all_equalprior.temporal_proximity_is_goodseqVsInsitu
Dependencies:arrangementsgmpiteratorsiterpcR6
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Finding the most likely originating tissue(s) and developmental stage(s) of RNASeq data | cellOrigins-package cellOrigins |
| Patterns of gene expression in Drosophila melanogaster embryos | BDGP_insitu_dmel_embryo |
| Diagnostic plots to explore seqVsInsitu results | diagnosticPlots diagnosticPlots.list diagnosticPlots.matrix |
| In situ discovery probability as a function of FPKM | discovery_probability |
| Calculates discovery probability by RNA in situ hybridisation given a sequencing signal | discovery.identic discovery.linear discovery.log |
| Faster comparisons between mixed tissue-specific RNA sequencing data and high-throughput RNA in situ hybridisation | iterating_seqVsInsitu |
| Assign a prior probability to a combination of anatomical terms | prior.all_equal prior.temporal_proximity_is_good |
| Determine the most likely source(s) of a tissue-specific RNAseq dataset | seqVsInsitu |
| Drosophila melanogaster embryo ventral nerve cord RNASeq coverage | vncMedianCoverage |
