Bioconductor Code Search

Found 840 results in 551 files, showing top 50 files (show more).

rnaEditr:inst/scripts/2-CreateRnaEditAndPhenoDFs.R: [ ]
104: cl <- makeCluster(detectCores()/2)

cellmigRation:R/all_functions_v8.R: [ ]
3604: #' @importFrom parallel detectCores
3618: max.cores <- parallel::detectCores()
3844: #' @importFrom parallel detectCores makeCluster clusterExport stopCluster
4156: #' @importFrom parallel detectCores makeCluster clusterExport
4406: max.cores <- parallel::detectCores()
4546: #' @importFrom parallel detectCores makeCluster clusterExport

MSnbase:NEWS.md: [ ]
1731: - enhanced parallel in DESCRIPTION and detectCores()

PADOG:R/padog.R: [ ]
223: ncores = parallel::detectCores()

sitadela:R/sitadela.R: [ ]
1894: ncores <- parallel::detectCores()

TOAST:R/cedar.R: [ ]
431: cores_num <- min(core.num, parallel::detectCores()) #detectCores() - 2

covRNA:R/stat.R: [ ]
27: stat <- function(ExprSet, R=NULL, L=NULL, Q=NULL, npermut=9999, padjust="BH", nrcor=detectCores()-1, exprvar=1) {

hiAnnotator:R/hiAnnotator.R: [ ]
220: #' length(sites.rd)/detectCores() or length(query)/getDoParWorkers()
251: length(sites.rd) / detectCores()

DECIPHER:R/TreeLine.R: [ ]
1989: processors <- detectCores()

sincell:R/sincell.R: [ ]
386: ...(60 bytes skipped)...ject, num_it=100, num_genes=as.integer(nrow(SincellObject[["expressionmatrix"]])0.5), cores=ifelse(detectCores()>=4, 4, detectCores*())){
485: ...(155 bytes skipped)...Data = T, baseLogTransformation=exp(1),pseudocounts.added.before.log.transformation=1, cores=ifelse(detectCores()>=4, 4, detectCores())){
627: ...(60 bytes skipped)...s <- function(SincellObject, method="own", num_it=100, fraction.cells.to.replace=0.15, cores=ifelse(detectCores()>=4, 4, detectCores())){
751: ...(80 bytes skipped)...nimum.geneset.size=50,p.value.assessment=TRUE,spearman.rank.threshold=0.5,num_it=1000, cores=ifelse(detectCores()>=4, 4, detectCores())){

cnvGSA:R/cnvGSA.R: [ ]
510: coreNum <- detectCores()
745: coreNum <- detectCores()

SynExtend:R/EvoWeaver-utils.R: [ ]
13: coresAvailable <- detectCores()

ChromSCape:R/preprocessing_filtering_reduction.R: [ ]
295: #' @importFrom parallel detectCores mclapply

CHRONOS:R/pathwayToGraph.R: [ ]
47: cores <- ifelse( N > detectCores()*10, 'default', 1 )

scde:R/functions.R: [ ]
1128: ...(90 bytes skipped)...ed = 5, min.count.threshold = 1, save.model.plots = TRUE, max.model.plots = 50, n.cores = parallel::detectCores(), min.size.entries = 2e3, min.fpm = 0, cor.method = "pearson", verbose = 0, fpm.estimate.trim = 0....(112 bytes skipped)...
1317: ...(54 bytes skipped)...L, trim = 0, prior = NULL, fit.genes=NULL, plot = TRUE, minimize.underdispersion = FALSE, n.cores = detectCores(), n.randomizations = 100, weight.k = 0.9, verbose = 0, weight.df.power = 1, smooth.df = -1, max.ad...(61 bytes skipped)...
1877: pagoda.pathway.wPCA <- function(varinfo, setenv, n.components = 2, n.cores = detectCores(), min.pathway.size = 10, max.pathway.size = 1e3, n.randomizations = 10, n.internal.shuffles = 0, n...(90 bytes skipped)...
2028: ...(74 bytes skipped)...clusters = 150, n.samples = 60, cor.method = "p", n.internal.shuffles = 0, n.starts = 10, n.cores = detectCores(), verbose = 0, plot = FALSE, show.random = FALSE, n.components = 1, method = "ward.D", secondary.c...(70 bytes skipped)...
2459: ...(67 bytes skipped)...LL, plot = FALSE, cluster.method = "complete", distance.threshold = 0.01, corr.power = 4, n.cores = detectCores(), abs = TRUE, ...) {

SeqArray:R/Internal.R: [ ]
364: ans <- detectCores() - 1L

scCB2:R/CB2FindCell.R: [ ]
453: Ncores = detectCores() - 2,
490: Ncores = detectCores() - 2,

MMDiff2:R/getPeakReads.R: [ ]
100: NCPUs <- detectCores()

adductomicsR:R/specSimPepId.R: [ ]
10: #' parallel::detectCores()
112: #' @usage specSimPepId(MS2Dir=NULL,nCores=parallel::detectCores(),

ILoReg:R/CoreMethods.R: [ ]
149: #' @importFrom parallel makeCluster detectCores stopCluster
252: cl <- makeCluster(detectCores(logical=TRUE)-1)

sccomp:R/utilities.R: [ ]
401: data_for_model, model, censoring_iteration = 1, cores = detectCores(), quantile = 0.95,

ccmap:R/query_combos.R: [ ]
76: ...(32 bytes skipped)...enes, drug_info = c('cmap', 'l1000'), method = c('average', 'ml'), include = NULL, ncores=parallel::detectCores()) {

ADaCGH2:R/ADaCGH-2.R: [ ]
214: mc.cores = detectCores(),
986: ## mc.cores = detectCores())
1056: mc.cores = floor(detectCores()/2)) {
1149: ## mc.cores = detectCores())
1159: mc.cores = mcc(reading.cores)) ## detectCores())
1223: ## with detectCores
1232: mc.cores = mcc(reading.cores)) ##detectCores())
1773: mc.cores = detectCores(),
2493: mc.cores = detectCores(),
2719: mc.cores = detectCores(),
2954: mc.cores = detectCores(),
3261: mc.cores = detectCores(),
3446: mc.cores = detectCores(),
3735: mc.cores = detectCores(),
3966: mc.cores = detectCores(),
5621: ## mc.cores = detectCores())
5624: ## mc.cores = detectCores())
5636: ## mc.cores = detectCores())
5770: ## mc.cores = 64) # detectCores())
6055: ## mc.cores = detectCores())
6059: ## mc.cores = detectCores())
6061: ## mc.cores = detectCores())
6063: ## mc.cores = detectCores())
6065: ## mc.cores = detectCores())
6067: ## mc.cores = detectCores())
6094: ## mc.cores = detectCores())

HarmonizR:R/main.r: [ ]
228: max_avail_cores <- parallel::detectCores()

VaSP:R/BMfinder.R: [ ]
20: #' @importFrom parallel mclapply detectCores
34: log = FALSE, cores = detectCores() - 1) {

ipdDb:inst/scripts/make-data.R: [ ]
187: ncores <- parallel::detectCores()/2
437: #' \item{\code{x$new(locusname, db_version, ncores = parallel::detectCores(),

SC3:R/CoreMethods.R: [ ]
118: #' @importFrom parallel detectCores
229: n_cores <- parallel::detectCores()

mitch:R/mitch.R: [ ]
1065: MANOVA <- function(x, genesets, minsetsize = 10, cores = detectCores() - 1,
1157: ANOVA <- function(x, genesets, minsetsize = 10, cores = detectCores() - 1,
1451: mitch_calc <- function(x, genesets, minsetsize = 10, cores = detectCores() - 1,

mitch:R/mitch.R: [ ]

1065: MANOVA <- function(x, genesets, minsetsize = 10, cores = detectCores() - 1,

1157: ANOVA <- function(x, genesets, minsetsize = 10, cores = detectCores() - 1,

1451: mitch_calc <- function(x, genesets, minsetsize = 10, cores = detectCores() - 1,

GenomicOZone:R/MD_perform_zoning.R: [ ]
74: #' @importFrom parallel detectCores makeCluster stopCluster parLapply

miRspongeR:R/miRspongeR.R: [ ]
341: cl <- makeCluster(detectCores() - 2)
1704: Res <- foreach(i = seq_len(nrow(index)), .export = c("dtHybrid", "makeCluster", "detectCores", "recommendation",
2136: "detectCores", "recommendation", "graphWeights", "parMM", "stopCluster", "clusterApply")) %dopar% {
2146: "detectCores", "recommendation", "graphWeights", "parMM", "stopCluster", "clusterApply")) %dopar% {

ramr:R/getAMR.R: [ ]
85: #' @importFrom parallel detectCores makeCluster stopCluster
106: cores=max(1,parallel::detectCores()-1),

branchpointer:R/predictBranchpoints.R: [ ]
216: maxCores <- parallel::detectCores()
506: maxCores <- parallel::detectCores()

ppcseq:R/utilities.R: [ ]
854: #' @importFrom parallel detectCores
857: detectCores() %>% as.integer
862: # parallel::detectCores() %>% as.integer %>% sum(-1)

rCGH:R/AllHelperFunctions.R: [ ]
570: maxCores <- detectCores()

DegNorm:R/coverage_cal_functions.R: [ ]
38: max.cores=detectCores(logical = FALSE)

SIMLR:R/SIMLR_Estimate_Number_of_Clusters.R: [ ]
19: #' @importFrom parallel stopCluster makeCluster detectCores clusterEvalQ parLapply
189: cores = as.integer(cores.ratio * (detectCores() - 1))

RiboDiPA:R/package.R: [ ]
6: cores <- detectCores(logical=FALSE)
211: cores <- detectCores(logical=FALSE)
353: if (is.null(cores)) cores <- detectCores(logical=FALSE)

GUIDEseq:R/getUniqueCleavageEvents.R: [ ]
157: #' @importFrom parallel makeCluster stopCluster detectCores
646: n.cores <- min(n.cores, detectCores() -1 )

DSS:R/DML.R: [ ]
19: ncores = max(detectCores() - 3, 1)
22: if(ncores > detectCores())

CausalR:R/RankTheHypotheses.r: [ ]
72: numCores <- parallel::detectCores() - 1

sigsquared:R/GeneSignature.R: [ ]
14: ## nCores <<- detectCores()

sitePath:R/sitesMinEntropy.R: [ ]
2: #' @importFrom parallel detectCores

TVTB:inst/shinyApp/server.R: [ ]
2563: min = 1, max = parallel::detectCores())
2572: min = 1, max = parallel::detectCores())

oppar:R/gsva.R: [ ]
646: detCor <- get('detectCores', envir=getNamespace('parallel'))
846: detCor <- get('detectCores', envir=getNamespace('parallel'))
968: detCor <- get('detectCores', envir=getNamespace('parallel'))
1059: detCor <- get('detectCores', envir=getNamespace('parallel'))

PERFect:R/utility_functions.R: [ ]
43: no_cores <- parallel::detectCores()-1

fcScan:R/getCluster.R: [ ]
212: if(threads %% 1 !=0 \|\| threads < 0 \|\| threads > detectCores()){
218: if(detectCores() >= length(unique(as.character(seqnames(x))))){
221: else if(detectCores() < length(unique(as.character(seqnames(x))))){
222: threads = detectCores()

CNVPanelizer:R/FolderAnalysis_functions.R: [ ]
1260: # # Use the detectCores() function to find the number of cores in system
1261: # no_cores <- detectCores()

GSgalgoR:R/galgo.R: [ ]
666: num_workers <- parallel::detectCores()

SparseSignatures:R/signatures.discovery.lasso.R: [ ]
97: cores <- as.integer((detectCores()-1))
501: cores <- as.integer((detectCores()-1))
1202: cores <- as.integer((detectCores()-1))
1429: cores <- as.integer((detectCores()-1))

netprioR:R/netprioR-functions.R: [ ]
11: #' @importFrom parallel detectCores
32: thresh = 1e-3, use.cg = TRUE, thresh.cg = 1e-5, nrestarts = 5, max.cores = detectCores(), verbose = FALSE) {

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Found 840 results in 551 files, showing top 50 files (show more).