Caught segfault when running MEDIPS package
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Guest User ★ 13k
@guest-user-4897
Last seen 10.3 years ago
Hi, I'm running MEDIPS package to analyze methylation sequencing data. I have many samples (from the same source and preprocessed the same way) and some of them are performing without problems but for some there is an error with segfault during the methylProfiling step. For some of the problematic samples it helps when I manually reload the saved normalized data object and rerun the code interactively but for one of the samples I still get the same error. The code, error and session info are given below. I would be very grateful for any help! genome <- c("BSgenome.Hsapiens.UCSC.hg19") pgenome <- "hg19" library(BSgenome.Hsapiens.UCSC.hg19) coverage.resolution <- 50 smoothing.extension <- 400 dat <- MEDIPS.readAlignedSequences(BSgenome=genome, file=paste(aDir, "/MEDIPS_input/",samples[i], "_MEDIPS-input.tsv", sep="")) dat <- MEDIPS.genomeVector(data=dat, bin_size=as.numeric(coverage.resolution), extend=as.numeric(smoothing.extension)) dat <- MEDIPS.getPositions(data=dat, pattern="CG") dat <- MEDIPS.couplingVector(data=dat, fragmentLength=as.numeric(fragment.length), func="count") dat <- MEDIPS.normalize(data=dat) roisFile <- paste(aDir, "/promoter_rois.xls", sep="") if(!file.exists(roisFile)){ library(rtracklayer) session <- browserSession() genome(session) <- pgenome query <- ucscTableQuery(session, "refGene") refGene <- getTable(query) sta <- refGene$txStart sta[refGene$strand=="+"] <- sta[refGene$strand=="+"]-1000 sta[refGene$strand=="-"] <- sta[refGene$strand=="-"]-500 sto <- refGene$txStart sto[refGene$strand=="+"] <- sta[refGene$strand=="+"]+500 sto[refGene$strand=="-"] <- sta[refGene$strand=="-"]+1000 rois <- unique(data.frame(refGene$chrom, sta, sto, make.unique(as.character(refGene$name)))) write.table(rois, file=roisFile, sep="\t", quote=F, col.names=F, row.names=F) rois <- read.table(roisFile, sep="\t", as.is=T) colnames(rois) <- c("refGene.chrom", "sta", "sto", "refGene.name") frames <- MEDIPS.methylProfiling(data1=dat, ROI_file=roisFile, math=mean, select=2) Preprocessing... Reading ROIs... Extract data according to given ROI... Methylation profile will be calculated on the ROI data set Analysed 39041 / 41310 *** caught segfault *** address 0x2aca1311f900, cause 'memory not mapped' Traceback: 1: .Call("roiprofile", input, as.numeric(select), as.matrix(ROI2), as.integer(chr_binposition), data1, data2, environment(wilcox.test), wilcox.test, environment(var), var, environment(math), math, t.test, environment(t.test), as.numeric(factor(chr_names(data1)))) 2: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning")) 3: suppressWarnings(.Call("roiprofile", input, as.numeric(select), as.matrix(ROI2), as.integer(chr_binposition), data1, data2, environment(wilcox.test), wilcox.test, environment(var), var, environment(math), math, t.test, environment(t.test), as.numeric(factor(chr_names(data1))))) 4: MEDIPS.methylProfiling(data1 = dat, ROI_file = roisFile, math = mean, select = 2) Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace Selection: -- output of sessionInfo(): R version 2.14.0 (2011-10-31) Platform: x86_64-redhat-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] MEDIPS_1.4.0 BSgenome.Hsapiens.UCSC.hg19_1.3.17 [3] BSgenome_1.22.0 Biostrings_2.22.0 [5] GenomicRanges_1.6.4 IRanges_1.12.5 loaded via a namespace (and not attached): [1] gtools_2.6.2 -- Sent via the guest posting facility at bioconductor.org.
Sequencing MEDIPS Sequencing MEDIPS • 1.4k views
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Oscar Rueda ▴ 40
@oscar-rueda-3347
Last seen 10.3 years ago
Hi Asta, I've had a similar error in the past; It was caused by chromosome names in the roi file not found in your data file. I would check that. Cheers, Oscar Oscar M. Rueda, PhD. Postdoctoral Research Fellow, Breast Cancer Functional Genomics. Cancer Research UK Cambridge Research Institute. Li Ka Shing Centre, Robinson Way. Cambridge CB2 0RE England On 10/1/12 14:13, "Asta Laiho [guest]" <guest at="" bioconductor.org=""> wrote: > > > Hi, > > I'm running MEDIPS package to analyze methylation sequencing data. I have many > samples (from the same source and preprocessed the same way) and some of them > are performing without problems but for some there is an error with segfault > during the methylProfiling step. For some of the problematic samples it helps > when I manually reload the saved normalized data object and rerun the code > interactively but for one of the samples I still get the same error. > > The code, error and session info are given below. I would be very grateful for > any help! > > > genome <- c("BSgenome.Hsapiens.UCSC.hg19") > pgenome <- "hg19" > library(BSgenome.Hsapiens.UCSC.hg19) > > coverage.resolution <- 50 > smoothing.extension <- 400 > > dat <- MEDIPS.readAlignedSequences(BSgenome=genome, file=paste(aDir, > "/MEDIPS_input/",samples[i], "_MEDIPS-input.tsv", sep="")) > dat <- MEDIPS.genomeVector(data=dat, bin_size=as.numeric(coverage.resolution), > extend=as.numeric(smoothing.extension)) > dat <- MEDIPS.getPositions(data=dat, pattern="CG") > dat <- MEDIPS.couplingVector(data=dat, > fragmentLength=as.numeric(fragment.length), func="count") > dat <- MEDIPS.normalize(data=dat) > > > roisFile <- paste(aDir, "/promoter_rois.xls", sep="") > if(!file.exists(roisFile)){ > library(rtracklayer) > session <- browserSession() > genome(session) <- pgenome > query <- ucscTableQuery(session, "refGene") > refGene <- getTable(query) > sta <- refGene$txStart > sta[refGene$strand=="+"] <- sta[refGene$strand=="+"]-1000 > sta[refGene$strand=="-"] <- sta[refGene$strand=="-"]-500 > sto <- refGene$txStart > sto[refGene$strand=="+"] <- sta[refGene$strand=="+"]+500 > sto[refGene$strand=="-"] <- sta[refGene$strand=="-"]+1000 > rois <- unique(data.frame(refGene$chrom, sta, sto, > make.unique(as.character(refGene$name)))) > write.table(rois, file=roisFile, sep="\t", quote=F, col.names=F, row.names=F) > rois <- read.table(roisFile, sep="\t", as.is=T) > colnames(rois) <- c("refGene.chrom", "sta", "sto", "refGene.name") > > frames <- MEDIPS.methylProfiling(data1=dat, ROI_file=roisFile, math=mean, > select=2) > > Preprocessing... > Reading ROIs... > Extract data according to given ROI... > Methylation profile will be calculated on the ROI data set > Analysed 39041 / 41310 > *** caught segfault *** > address 0x2aca1311f900, cause 'memory not mapped' > > Traceback: > 1: .Call("roiprofile", input, as.numeric(select), as.matrix(ROI2), > as.integer(chr_binposition), data1, data2, environment(wilcox.test), > wilcox.test, environment(var), var, environment(math), math, t.test, > environment(t.test), as.numeric(factor(chr_names(data1)))) > 2: withCallingHandlers(expr, warning = function(w) > invokeRestart("muffleWarning")) > 3: suppressWarnings(.Call("roiprofile", input, as.numeric(select), > as.matrix(ROI2), as.integer(chr_binposition), data1, data2, > environment(wilcox.test), wilcox.test, environment(var), var, > environment(math), math, t.test, environment(t.test), > as.numeric(factor(chr_names(data1))))) > 4: MEDIPS.methylProfiling(data1 = dat, ROI_file = roisFile, math = mean, > select = 2) > > Possible actions: > 1: abort (with core dump, if enabled) > 2: normal R exit > 3: exit R without saving workspace > 4: exit R saving workspace > Selection: > > > -- output of sessionInfo(): > > R version 2.14.0 (2011-10-31) > Platform: x86_64-redhat-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] MEDIPS_1.4.0 BSgenome.Hsapiens.UCSC.hg19_1.3.17 > [3] BSgenome_1.22.0 Biostrings_2.22.0 > [5] GenomicRanges_1.6.4 IRanges_1.12.5 > > loaded via a namespace (and not attached): > [1] gtools_2.6.2 > > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor NOTICE AND DISCLAIMER This e-mail (including any attachments) is intended for ...{{dropped:16}}
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Hi, indeed there might be a problem with a region of interest included in your ROI file ('rois'). The MEDIPS output indicates that there is a problem with the given roi at line 39041 (see your output below). It might be worthwhile to check this roi (or the immediate neighbours) for consistency. It is likely that - the roi is of length 0 or of negative length (i.e. if start position <= stop position) - the genomic coordinates of the roi are outside of the length of the chromosome - the chromosome of the roi is not represented by the MeDIP-seq data (e.g. there are no chrM short reads given but you have chrM in your ROIs). Unfortunately, these cases are not caught internally by MEDIPS and the R session quits what is a very ugly behaviour. Please apologise this 'bad programming' (but we are working on an improved and completely revised version). In case to cannot narrow down your error to a suspicious roi, please post again and we will try to figure out the reason in detail. Best, Lukas On Tue, 10 Jan 2012 14:38:39 +0000, Oscar Rueda <oscar.rueda at="" cancer.org.uk=""> wrote: > Hi Asta, > > I've had a similar error in the past; It was caused by chromosome names in > the roi file not found in your data file. I would check that. > > Cheers, > Oscar > > > Oscar M. Rueda, PhD. > Postdoctoral Research Fellow, Breast Cancer Functional Genomics. > Cancer Research UK Cambridge Research Institute. > Li Ka Shing Centre, Robinson Way. > Cambridge CB2 0RE > England > > > > > > On 10/1/12 14:13, "Asta Laiho [guest]" <guest at="" bioconductor.org=""> wrote: > >> >> >> Hi, >> >> I'm running MEDIPS package to analyze methylation sequencing data. I >> have many >> samples (from the same source and preprocessed the same way) and some of >> them >> are performing without problems but for some there is an error with >> segfault >> during the methylProfiling step. For some of the problematic samples it >> helps >> when I manually reload the saved normalized data object and rerun the >> code >> interactively but for one of the samples I still get the same error. >> >> The code, error and session info are given below. I would be very >> grateful for >> any help! >> >> >> genome <- c("BSgenome.Hsapiens.UCSC.hg19") >> pgenome <- "hg19" >> library(BSgenome.Hsapiens.UCSC.hg19) >> >> coverage.resolution <- 50 >> smoothing.extension <- 400 >> >> dat <- MEDIPS.readAlignedSequences(BSgenome=genome, file=paste(aDir, >> "/MEDIPS_input/",samples[i], "_MEDIPS-input.tsv", sep="")) >> dat <- MEDIPS.genomeVector(data=dat, >> bin_size=as.numeric(coverage.resolution), >> extend=as.numeric(smoothing.extension)) >> dat <- MEDIPS.getPositions(data=dat, pattern="CG") >> dat <- MEDIPS.couplingVector(data=dat, >> fragmentLength=as.numeric(fragment.length), func="count") >> dat <- MEDIPS.normalize(data=dat) >> >> >> roisFile <- paste(aDir, "/promoter_rois.xls", sep="") >> if(!file.exists(roisFile)){ >> library(rtracklayer) >> session <- browserSession() >> genome(session) <- pgenome >> query <- ucscTableQuery(session, "refGene") >> refGene <- getTable(query) >> sta <- refGene$txStart >> sta[refGene$strand=="+"] <- sta[refGene$strand=="+"]-1000 >> sta[refGene$strand=="-"] <- sta[refGene$strand=="-"]-500 >> sto <- refGene$txStart >> sto[refGene$strand=="+"] <- sta[refGene$strand=="+"]+500 >> sto[refGene$strand=="-"] <- sta[refGene$strand=="-"]+1000 >> rois <- unique(data.frame(refGene$chrom, sta, sto, >> make.unique(as.character(refGene$name)))) >> write.table(rois, file=roisFile, sep="\t", quote=F, col.names=F, >> row.names=F) >> rois <- read.table(roisFile, sep="\t", as.is=T) >> colnames(rois) <- c("refGene.chrom", "sta", "sto", "refGene.name") >> >> frames <- MEDIPS.methylProfiling(data1=dat, ROI_file=roisFile, math=mean, >> select=2) >> >> Preprocessing... >> Reading ROIs... >> Extract data according to given ROI... >> Methylation profile will be calculated on the ROI data set >> Analysed 39041 / 41310 >> *** caught segfault *** >> address 0x2aca1311f900, cause 'memory not mapped' >> >> Traceback: >> 1: .Call("roiprofile", input, as.numeric(select), as.matrix(ROI2), >> as.integer(chr_binposition), data1, data2, environment(wilcox.test), >> wilcox.test, environment(var), var, environment(math), math, t.test, >> environment(t.test), as.numeric(factor(chr_names(data1)))) >> 2: withCallingHandlers(expr, warning = function(w) >> invokeRestart("muffleWarning")) >> 3: suppressWarnings(.Call("roiprofile", input, as.numeric(select), >> as.matrix(ROI2), as.integer(chr_binposition), data1, data2, >> environment(wilcox.test), wilcox.test, environment(var), var, >> environment(math), math, t.test, environment(t.test), >> as.numeric(factor(chr_names(data1))))) >> 4: MEDIPS.methylProfiling(data1 = dat, ROI_file = roisFile, math = mean, >> select = 2) >> >> Possible actions: >> 1: abort (with core dump, if enabled) >> 2: normal R exit >> 3: exit R without saving workspace >> 4: exit R saving workspace >> Selection: >> >> >> -- output of sessionInfo(): >> >> R version 2.14.0 (2011-10-31) >> Platform: x86_64-redhat-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=C LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] MEDIPS_1.4.0 BSgenome.Hsapiens.UCSC.hg19_1.3.17 >> [3] BSgenome_1.22.0 Biostrings_2.22.0 >> [5] GenomicRanges_1.6.4 IRanges_1.12.5 >> >> loaded via a namespace (and not attached): >> [1] gtools_2.6.2 >> >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > NOTICE AND DISCLAIMER > This e-mail (including any attachments) is intended for ...{{dropped:16}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
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Hi, Many thanks for your advice, the problem indeed seems to be related to coordinates missing for the specific sample. - Asta On Jan 11, 2012, at 12:53 AM, chavez wrote: > > Hi, > > indeed there might be a problem with a region of interest included in your > ROI file ('rois'). The MEDIPS output indicates that there is a problem with > the given roi at line 39041 (see your output below). It might be worthwhile > to check this roi (or the immediate neighbours) for consistency. > > It is likely that > - the roi is of length 0 or of negative length (i.e. if start position <= > stop position) > - the genomic coordinates of the roi are outside of the length of the > chromosome > - the chromosome of the roi is not represented by the MeDIP-seq data (e.g. > there are no chrM short reads given but you have chrM in your ROIs). > > Unfortunately, these cases are not caught internally by MEDIPS and the R > session quits what is a very ugly behaviour. Please apologise this 'bad > programming' (but we are working on an improved and completely revised > version). > > In case to cannot narrow down your error to a suspicious roi, please post > again and we will try to figure out the reason in detail. > > Best, > Lukas > > > On Tue, 10 Jan 2012 14:38:39 +0000, Oscar Rueda > <oscar.rueda at="" cancer.org.uk=""> > wrote: >> Hi Asta, >> >> I've had a similar error in the past; It was caused by chromosome names > in >> the roi file not found in your data file. I would check that. >> >> Cheers, >> Oscar >> >> >> Oscar M. Rueda, PhD. >> Postdoctoral Research Fellow, Breast Cancer Functional Genomics. >> Cancer Research UK Cambridge Research Institute. >> Li Ka Shing Centre, Robinson Way. >> Cambridge CB2 0RE >> England >> >> >> >> >> >> On 10/1/12 14:13, "Asta Laiho [guest]" <guest at="" bioconductor.org=""> wrote: >> >>> >>> >>> Hi, >>> >>> I'm running MEDIPS package to analyze methylation sequencing data. I >>> have many >>> samples (from the same source and preprocessed the same way) and some > of >>> them >>> are performing without problems but for some there is an error with >>> segfault >>> during the methylProfiling step. For some of the problematic samples it >>> helps >>> when I manually reload the saved normalized data object and rerun the >>> code >>> interactively but for one of the samples I still get the same error. >>> >>> The code, error and session info are given below. I would be very >>> grateful for >>> any help! >>> >>> >>> genome <- c("BSgenome.Hsapiens.UCSC.hg19") >>> pgenome <- "hg19" >>> library(BSgenome.Hsapiens.UCSC.hg19) >>> >>> coverage.resolution <- 50 >>> smoothing.extension <- 400 >>> >>> dat <- MEDIPS.readAlignedSequences(BSgenome=genome, file=paste(aDir, >>> "/MEDIPS_input/",samples[i], "_MEDIPS-input.tsv", sep="")) >>> dat <- MEDIPS.genomeVector(data=dat, >>> bin_size=as.numeric(coverage.resolution), >>> extend=as.numeric(smoothing.extension)) >>> dat <- MEDIPS.getPositions(data=dat, pattern="CG") >>> dat <- MEDIPS.couplingVector(data=dat, >>> fragmentLength=as.numeric(fragment.length), func="count") >>> dat <- MEDIPS.normalize(data=dat) >>> >>> >>> roisFile <- paste(aDir, "/promoter_rois.xls", sep="") >>> if(!file.exists(roisFile)){ >>> library(rtracklayer) >>> session <- browserSession() >>> genome(session) <- pgenome >>> query <- ucscTableQuery(session, "refGene") >>> refGene <- getTable(query) >>> sta <- refGene$txStart >>> sta[refGene$strand=="+"] <- sta[refGene$strand=="+"]-1000 >>> sta[refGene$strand=="-"] <- sta[refGene$strand=="-"]-500 >>> sto <- refGene$txStart >>> sto[refGene$strand=="+"] <- sta[refGene$strand=="+"]+500 >>> sto[refGene$strand=="-"] <- sta[refGene$strand=="-"]+1000 >>> rois <- unique(data.frame(refGene$chrom, sta, sto, >>> make.unique(as.character(refGene$name)))) >>> write.table(rois, file=roisFile, sep="\t", quote=F, col.names=F, >>> row.names=F) >>> rois <- read.table(roisFile, sep="\t", as.is=T) >>> colnames(rois) <- c("refGene.chrom", "sta", "sto", "refGene.name") >>> >>> frames <- MEDIPS.methylProfiling(data1=dat, ROI_file=roisFile, > math=mean, >>> select=2) >>> >>> Preprocessing... >>> Reading ROIs... >>> Extract data according to given ROI... >>> Methylation profile will be calculated on the ROI data set >>> Analysed 39041 / 41310 >>> *** caught segfault *** >>> address 0x2aca1311f900, cause 'memory not mapped' >>> >>> Traceback: >>> 1: .Call("roiprofile", input, as.numeric(select), as.matrix(ROI2), >>> as.integer(chr_binposition), data1, data2, environment(wilcox.test), >>> wilcox.test, environment(var), var, environment(math), math, > t.test, >>> environment(t.test), as.numeric(factor(chr_names(data1)))) >>> 2: withCallingHandlers(expr, warning = function(w) >>> invokeRestart("muffleWarning")) >>> 3: suppressWarnings(.Call("roiprofile", input, as.numeric(select), >>> as.matrix(ROI2), as.integer(chr_binposition), data1, data2, >>> environment(wilcox.test), wilcox.test, environment(var), var, >>> environment(math), math, t.test, environment(t.test), >>> as.numeric(factor(chr_names(data1))))) >>> 4: MEDIPS.methylProfiling(data1 = dat, ROI_file = roisFile, math = > mean, >>> select = 2) >>> >>> Possible actions: >>> 1: abort (with core dump, if enabled) >>> 2: normal R exit >>> 3: exit R without saving workspace >>> 4: exit R saving workspace >>> Selection: >>> >>> >>> -- output of sessionInfo(): >>> >>> R version 2.14.0 (2011-10-31) >>> Platform: x86_64-redhat-linux-gnu (64-bit) >>> >>> locale: >>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >>> [7] LC_PAPER=C LC_NAME=C >>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] MEDIPS_1.4.0 > BSgenome.Hsapiens.UCSC.hg19_1.3.17 >>> [3] BSgenome_1.22.0 Biostrings_2.22.0 >>> [5] GenomicRanges_1.6.4 IRanges_1.12.5 >>> >>> loaded via a namespace (and not attached): >>> [1] gtools_2.6.2 >>> >>> >>> -- >>> Sent via the guest posting facility at bioconductor.org. >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> >> NOTICE AND DISCLAIMER >> This e-mail (including any attachments) is intended for > ...{{dropped:16}} >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor
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