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| Package: scellpam | ||
| Type: Package | ||
| Title: Applying Partitioning Around Medoids to Single Cell Data with | ||
| High Number of Cells | ||
| Version: 1.4 | ||
| Date: 2022-10-30 | ||
| Author: Juan Domingo [aut, cre] (<https://orcid.org/0000-0003-4728-6256>), | ||
| Guillermo Ayala [ctb] (<https://orcid.org/0000-0002-6231-2865>), | ||
| Spanish Ministry of Science and Innovation, MCIN/AEI | ||
| <doi:10.13039/501100011033> [fnd] | ||
| Maintainer: Juan Domingo <Juan.Domingo@uv.es> | ||
| Authors@R: c(person("Juan","Domingo", email = "Juan.Domingo@uv.es", role=c("aut","cre"), comment=c(ORCID="0000-0003-4728-6256")), | ||
| person("Guillermo","Ayala", email = "Guillermo.Ayala@uv.es", role=c("ctb"), comment=c(ORCID="0000-0002-6231-2865")), | ||
| person("Spanish Ministry of Science and Innovation, MCIN/AEI <doi:10.13039/501100011033>", role=c("fnd"))) | ||
| Description: PAM (Partitioning Around Medoids) algorithm application to samples of single cell sequencing techniques | ||
| with a high number of cells (as many as the computer memory allows). The package uses a binary format to | ||
| store matrices (either full, sparse or symmetric) in files written in the disk that can contain any data type | ||
| (not just double) which allows its manipulation when memory is sufficient to load them as int or float, but not | ||
| as double. The PAM implementation is done in parallel, using several/all the cores of the machine, if it has them. | ||
| This package shares a great part of its code with packages 'jmatrix' and 'parallelpam' but their functionality is | ||
| included here so there is no need to install them. | ||
| License: GPL (>= 2) | ||
| Imports: Rcpp (>= 1.0.8), memuse (>= 4.2.1), cluster (>= 2.1.4) | ||
| LinkingTo: Rcpp | ||
| RoxygenNote: 7.2.1 | ||
| Encoding: UTF-8 | ||
| Suggests: rmarkdown, knitr, DuoClustering2018, scater, splatter | ||
| VignetteBuilder: knitr | ||
| NeedsCompilation: yes | ||
| Packaged: 2022-11-26 18:54:29 UTC; jdomingo | ||
| Repository: CRAN | ||
| Date/Publication: 2022-11-28 10:10:02 UTC |
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| 809219a7e948ab5b491523189c57b8b9 *DESCRIPTION | ||
| ee8bb5792f2612253a2945343e977e88 *NAMESPACE | ||
| 8226bd9eacba89b9265373bcf9c3aa84 *R/RcppExports.R | ||
| 7547dc51b702c81fe4c673f51b9369da *build/vignette.rds | ||
| 287eef3934c26f8292168e865fc65090 *inst/doc/jmatrixsc.R | ||
| 6271c1247304e099576888065efb8774 *inst/doc/jmatrixsc.Rmd | ||
| f4c1741a6e2d8fbd6b9ff59afd87b6fe *inst/doc/jmatrixsc.html | ||
| 4f1033cae48be034ce4fac83c3abb393 *inst/doc/parallelpamsc.R | ||
| 3f27fab17633a3768cc317a86a11b75c *inst/doc/parallelpamsc.Rmd | ||
| 68021b7d2d29a042546ec0638f413661 *inst/doc/parallelpamsc.html | ||
| a6ae6e136c036152f07a54fc31787d0a *inst/doc/scellpam.R | ||
| 79dfd66299affda2cdbf93488ca1d734 *inst/doc/scellpam.Rmd | ||
| b34f7b387569d3513ecd4b3f8360962c *inst/doc/scellpam.html | ||
| 3ac15e1a60a0f6cabac5f8c73aa9bccd *inst/include/debugpar.h | ||
| b7d4e487db41a240fb821aff1681524c *inst/include/diftimehelper.h | ||
| eb95da38fc3e8bee2f6f4482db71ab59 *inst/include/dissimmat.h | ||
| 32df6f28ec0288f4d3548d9604eec9d5 *inst/include/fastpam.h | ||
| 64ac89d0b0c5f69a8620498aca7f03e2 *inst/include/fullmatrix.h | ||
| 2f8ffeb8f4201af149b901faf1bd5dec *inst/include/jmatrix.h | ||
| 9e3ae907bd1b596e82e73b854a06ddd4 *inst/include/matmetadata.h | ||
| 88b4a2bd69bd4a7590c5e65061f20850 *inst/include/memhelper.h | ||
| c77cbe89d1474ab5a16a747a0c069c1a *inst/include/silhouette.h | ||
| 26a21b4b82d56089cb9916b992123644 *inst/include/sparsematrix.h | ||
| 6cbe88c3b4937d4a072433a853be7c2f *inst/include/symmetricmatrix.h | ||
| af8af0d4d5d52892def11b0194b98853 *inst/include/templatemacros.h | ||
| e453255e14e21f7626a98e94d01fcf27 *inst/include/threadhelper.h | ||
| 13fb2b1fb3dc71aefbc64eec35ca5897 *man/ApplyPAM.Rd | ||
| 1302b44ef1d1207371069f3e7fce9507 *man/BuildAbundanceMatrix.Rd | ||
| 9c4098ce23cf29a929347333356213bd *man/CalcAndWriteDissimilarityMatrix.Rd | ||
| d3f514108ff65d7d8b31085cc9156790 *man/CalculateSilhouette.Rd | ||
| ba0a030f4a111b7b575b351d656f5eef *man/ClassifAsDataFrame.Rd | ||
| 894cfef4f83831dcf15fea819d5a862a *man/CsvToJMat.Rd | ||
| c6edeb639e299f70f03383a3f9296a18 *man/FilterBySilhouetteQuantile.Rd | ||
| 686a2a0c4241a8c2ba4a607681ac9bc7 *man/FilterBySilhouetteThreshold.Rd | ||
| ddb24828fdf9ee1befffa5becb8d95aa *man/FilterJMatByName.Rd | ||
| 08d218f1d393f3a143a01684ab18cda3 *man/GetJCol.Rd | ||
| d464a3939561659e626f13f8e0e7ae14 *man/GetJColByName.Rd | ||
| ad8805d7edc6d850c3109c85fa3014f0 *man/GetJColNames.Rd | ||
| 850a9d56fc3836588238eef03f9d6b6e *man/GetJManyCols.Rd | ||
| 8fcef375004fa74bd94235876edc0c77 *man/GetJManyColsByNames.Rd | ||
| c39de862e884cc59f3809f3ce349c0bd *man/GetJManyRows.Rd | ||
| efb25b2e39dde86feb2d4f4afb3eddba *man/GetJManyRowsByNames.Rd | ||
| 4f3dd7f15aefeaa5e6b869ff1d6982e9 *man/GetJNames.Rd | ||
| b93b75cf0f3d0e2d99778635ef551921 *man/GetJRow.Rd | ||
| 342074145dbc130a6baece3523593302 *man/GetJRowByName.Rd | ||
| 37d880ca345da2097cc7288a1338ec2e *man/GetJRowNames.Rd | ||
| e877b9bd64d95a5f3590f065a6de79b9 *man/GetSeuratGroups.Rd | ||
| 6b1d6eb3d3f2fe76f4b600edc1378a0b *man/GetSubdiag.Rd | ||
| 7ba84c9659589880cdc1b95b8f176cd6 *man/GetTD.Rd | ||
| 5d4ee21256183eaf61dacf1ad5dd4697 *man/JMatInfo.Rd | ||
| 9659a9526a4948f75902f5c4eca8d9a0 *man/JMatToCsv.Rd | ||
| 033b4915dee9ac5d560f46c1df9523b3 *man/JWriteBin.Rd | ||
| 0c104e27ea1d9c3ada9ec57b71437970 *man/NumSilToClusterSil.Rd | ||
| ec6c1226482c3251abd917b4545bcd23 *man/SceToJMat.Rd | ||
| 3183361d938aa858c5524cc46026ee9c *man/ScellpamSetDebug.Rd | ||
| a2e2f7b703ab20679d887a5fa525a0c7 *man/dgCMatToJMat.Rd | ||
| 7b93da85af7f02f533a8ac768833ded5 *src/Makevars | ||
| 5b1be82438d1868566e8503f75ca5bb8 *src/RcppExports.cpp | ||
| 0c79b1c4cacb141747699af7e69b249b *src/buildresults.cpp | ||
| 46025a8dcb0464fa8fa9c03a4e64c627 *src/datatobinmat.cpp | ||
| 033ec5ceedbdb499cfc5b203831c713f *src/debugpar.cpp | ||
| 4d1e965f323b36898d67ad3c7c061196 *src/diftimehelper.cpp | ||
| 77e0e4437a70be5139b0cb34d53090aa *src/dissimmat.cpp | ||
| 8ccbd0a8efeb4dcf208339d5d0fbdfcb *src/dissimmat_full.cpp | ||
| 8d1f0a3be3cb78ccf7062e5baa8bf18e *src/dissimmat_sparse.cpp | ||
| 8753103c933760a2dff57561c77ffca8 *src/fastpam.cpp | ||
| 60f4567a3c377a712881a73b2bc476bc *src/filtersil.cpp | ||
| 17ae5de1ecfb77eb54f4ac330ddd06f7 *src/fullmatrix.cpp | ||
| da0d583bea225db104b12fe44f667b7b *src/jmatrix.cpp | ||
| c6f4cc901ac914e095e8966a7001b30a *src/jmatrixaux.cpp | ||
| adb00bbe102e9d6ea5fbd9ddd1da9217 *src/mainfastpam.cpp | ||
| 4ca01985aeb35b36df61807f31d60cf0 *src/matgetcols.cpp | ||
| 6ad22c7de313a21783fd774646513537 *src/matgetdiag.cpp | ||
| 4c030d1983ba5db8f3a13bdea4281ca5 *src/matgetrows.cpp | ||
| e8cf05757a5bd1f34b416faee98f7223 *src/matinfo.cpp | ||
| ea77cf4b4545fb7192fc957ef29bb244 *src/matmetadata.cpp | ||
| 7c3859f609734aba009aa60af45fbeb0 *src/matwrite.cpp | ||
| ed0d29c45ee0f9a2e1251b68be60e1a5 *src/memhelper.cpp | ||
| 52e43001d0dfca9c268ce7215585072f *src/silhouette.cpp | ||
| 2a52c43c3358891f3c5e7db1cefab08a *src/sparsematrix.cpp | ||
| 70ff45e046a273f79ffd8a5b68aecc67 *src/symmetricmatrix.cpp | ||
| c65fb001ca293a7b3f05c40496681ff0 *src/threadhelper.cpp | ||
| e273aaff15de6c63e649a5ffc20bc442 *vignettes/extdata/Trapnell_remain_genes.csv | ||
| f93611dd960ef5b1e6eeeaaee2e8df5b *vignettes/extdata/conquer_GSE52529_Trapnell_sample.csv | ||
| 6271c1247304e099576888065efb8774 *vignettes/jmatrixsc.Rmd | ||
| 3f27fab17633a3768cc317a86a11b75c *vignettes/parallelpamsc.Rmd | ||
| 79dfd66299affda2cdbf93488ca1d734 *vignettes/scellpam.Rmd | ||
| 774874d61fb4e137e80a3a1606629731 *vignettes/scellpam.bib |
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| export(ApplyPAM) | ||
| export(BuildAbundanceMatrix) | ||
| export(CalcAndWriteDissimilarityMatrix) | ||
| export(CalculateSilhouette) | ||
| export(ClassifAsDataFrame) | ||
| export(CsvToJMat) | ||
| export(FilterBySilhouetteQuantile) | ||
| export(FilterBySilhouetteThreshold) | ||
| export(FilterJMatByName) | ||
| export(GetJCol) | ||
| export(GetJColByName) | ||
| export(GetJColNames) | ||
| export(GetJManyCols) | ||
| export(GetJManyColsByNames) | ||
| export(GetJManyRows) | ||
| export(GetJManyRowsByNames) | ||
| export(GetJNames) | ||
| export(GetJRow) | ||
| export(GetJRowByName) | ||
| export(GetJRowNames) | ||
| export(GetSeuratGroups) | ||
| export(GetSubdiag) | ||
| export(GetTD) | ||
| export(JMatInfo) | ||
| export(JMatToCsv) | ||
| export(JWriteBin) | ||
| export(NumSilToClusterSil) | ||
| export(SceToJMat) | ||
| export(ScellpamSetDebug) | ||
| export(dgCMatToJMat) | ||
| importFrom(memuse,Sys.meminfo) | ||
| importFrom(memuse,Sys.swapinfo) | ||
| useDynLib(scellpam, .registration=TRUE) | ||
| importFrom(Rcpp, evalCpp) |
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