Package: MouseFM 1.17.0
Matthias Munz
MouseFM: In-silico methods for genetic finemapping in inbred mice
This package provides methods for genetic finemapping in inbred mice by taking advantage of their very high homozygosity rate (>95%).
Authors:
MouseFM_1.17.0.tar.gz
MouseFM_1.17.0.zip(r-4.5)MouseFM_1.17.0.zip(r-4.4)MouseFM_1.17.0.zip(r-4.3)
MouseFM_1.17.0.tgz(r-4.4-any)MouseFM_1.17.0.tgz(r-4.3-any)
MouseFM_1.17.0.tar.gz(r-4.5-noble)MouseFM_1.17.0.tar.gz(r-4.4-noble)
MouseFM_1.17.0.tgz(r-4.4-emscripten)MouseFM_1.17.0.tgz(r-4.3-emscripten)
MouseFM.pdf |MouseFM.html✨
MouseFM/json (API)
NEWS
| # Install 'MouseFM' in R: |
| install.packages('MouseFM', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/matmu/mousefm/issues
On BioConductor:MouseFM-1.15.5(bioc 3.20)MouseFM-1.14.6(bioc 3.19)
geneticssnpgenetargetvariantannotationgenomicvariationmultiplecomparisonsystemsbiologymathematicalbiologypatternlogicgenepredictionbiomedicalinformaticsfunctionalgenomicsfinemapgene-candidatesinbred-miceinbred-strainsmouseqtlqtl-mapping
Last updated 23 days agofrom:16b409cd36. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win | NOTE | Oct 31 2024 |
| R-4.5-linux | NOTE | Oct 31 2024 |
| R-4.4-win | NOTE | Oct 31 2024 |
| R-4.4-mac | NOTE | Oct 31 2024 |
| R-4.3-win | NOTE | Oct 31 2024 |
| R-4.3-mac | NOTE | Oct 31 2024 |
Exports:annotate_consequencesannotate_mouse_genesavail_chromosomesavail_consequencesavail_strainsdf2GRangesfetchfinemapget_topgetURLGRanges2dfprioref_genomesetURLvis_reduction_factors
Dependencies:AnnotationDbiaskpassBiobaseBiocFileCacheBiocGenericsbiomaRtBiostringsbitbit64blobcachemclicolorspacecpp11crayoncurldata.tableDBIdbplyrdigestdplyrfansifarverfastmapfilelockgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablegtoolshmshttrhttr2IRangesisobandjsonliteKEGGRESTlabelinglatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrplyrpngprettyunitsprogresspurrrR6rappdirsRColorBrewerRcppreshape2rlangrlistRSQLiteS4VectorsscalesstringistringrsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXMLxml2XVectoryamlzlibbioc
Fetch homozygous genotypes of inbred mouse strains
Rendered fromfetch.Rmdusingknitr::rmarkdownon Oct 30 2024.Last update: 2020-06-08
Started: 2020-05-18
Finemapping of genetic regions in inbred mice
Rendered fromfinemap.Rmdusingknitr::rmarkdownon Oct 30 2024.Last update: 2020-06-08
Started: 2020-05-18
Prioritization of inbred mouse strains for resolving genetic regions
Rendered fromprio.Rmdusingknitr::rmarkdownon Oct 30 2024.Last update: 2020-06-08
Started: 2020-05-18
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Annotate with consequences | annotate_consequences |
| Annotate with genes | annotate_mouse_genes |
| Available chromosomes | avail_chromosomes |
| Available consequences | avail_consequences |
| Available strains | avail_strains |
| Data frame to GenomicRanges::GRanges object | df2GRanges |
| Fetch | fetch |
| Finemapping of genetic regions | finemap |
| Best strain combinations | get_top |
| Get backend service url | getURL |
| GenomicRanges::GRanges object to data frame | GRanges2df |
| Prioritization of inbred mouse strains for refining genetic regions | prio |
| Reference genome version | ref_genome |
| Set backend service url | setURL |
| Visualize | vis_reduction_factors |
