Bioconductor Forum

how to make the classic plots you see in GO analysis, like (picked from random papers) - [Bar charts (or possibly pie charts too)][3] - [A graph including and comparing different enrichment factors with circles][4] - [Something

go enrichment gene ontology goseq go

updated 6.3 years ago • Raito92

215 1_209363247 1_209995470 In this dataset, the first column is the number of segment, the second column is representing the number of SNPs per segment, and the third and fourth columns are representing...the smallest and largest SNPs number for each segment. I should note that the values of the third and fourth columns are the combination of the chromosome...number an…

annotation

updated 6.7 years ago • ari_sh70

<div class="preformatted">> > dear list, > > > > i'd like to know how can i download the conservation track for several > > genomic ranges belonging to different chromosome sequences > > This is not supported yet, mostly because whenever people have multiple > regions, they have a...can i download the conservation …

rtracklayer rtracklayer

updated 12.8 years ago • Dario Strbenac

Hi all, I am analyzing H2AZ ChIP seq data. I have the dba.report and dba.peakset which give chromosome number and peak position of differential peaks. I would like to get list of genes corresponding to those peaks

diffbind

updated 7.3 years ago • Bordiya

_cell\_names=FALSE), there are 4 isolated clusters which not have connections with other clusters number.  Is there any parameter wrong in my functions?   (2) Next, I intend to use the TSCANorder() function to get the...TSCANorder(mclustobj = lpsmclust, MSTorder = NULL, orderonly = T, flip = F, listbranch = F) But the number of elements in lpsorder is 10404 , however,…

TSCAN software error

updated 8.6 years ago • yancychy

help me? With thanks, Xavier \#./boost/utility/base\_from\_member.hpp:xxx:xx: warning: variadic templates only available with -std=c++11 or -std=gnu++11  template<typename ...T> \#./boost/thread/detail/invoke.hpp:xxx:xx: warning...variadic templates only available with -std=c++11 or -std=gnu++11      invoke(Ret(\*f)(Args... ), B…

mzr r installation

updated 8.8 years ago • microalgues

output$end.start and output$num.mark=0 and output$seg.mean=NA. In my case, it seems to be caused by "chromosomes" (contigs) with empty copy number data point (NAs). Here is a minimal example to try and illustrate the problem: &nbsp

DNAcopy dnacopy

updated 8.4 years ago • Alexandre Kuhn

I'm working with the following R code where I'm returning gene ontology terms pertinent to the biological process (BP) category: <pre> > source("https://bioconductor.org/biocLite.R") > biocLite("mygene") > xli <- c('BRCA1', 'BRCA2', 'SOX2', 'MYC') > res <- queryMany(xli, scopes='symbol', fields=c('go'), species='rat') Finis…

software error mygene gene ontology R

updated 8.5 years ago • Bohdan Khomtchouk

a conceptual question. I am trying to study the effects of a large-scale (100 mb; > 1,000 genes) chromosomal inversion on differential ATAC-seq peaks in two genotypes: in animals that are hets for the inversion, and those...my count matrix, I see many more differential peaks (>10,000 as tested by a basic t-test) on the chromosome with the inversion that are significant after a FDR c…

deseq2 normalization

updated 6.2 years ago • jrmerri

I have a list of variants in the format of NM_xxx.x:c.xxG>C that I need to translate to their chromosomal position as the corresponding NC_xxx.y:g.xxxC>G file. Is there a way to perform this conversion using a Bioconductor

refseq Bioconductor conversion

updated 5.1 years ago • heiko_kin

genome bisulfite sequencing dataset. I have a data table with one row per CpG and columns for: 1. chromosome 2. position 3. number of reads supporting an unmethylated CpG (U) 3. number of reads supporting a methylated CpG (M) Is

Sequencing Alignment bsseq Sequencing Alignment bsseq

updated 13.0 years ago • Martin Aryee

ILMN_1250814 ILMN_1257855 ILMN_2537948 ILMN_3144164 ILMN_2636200 what is the best way to fetch the chromosomal location of those ( chr: start :end)? Many thanks Nathalie -- The Wellcome Trust Sanger Institute is operated by Genome...Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 E…

updated 14.6 years ago • nac

class="preformatted">Dear List Is there currently any package (or way) allowing to associate KEGG K numbers (K02995) to pathways (ko03011) or ec. numbers? Thanks, Fabian ! [[alternative HTML version deleted]] </div

Pathways Pathways

updated 15.4 years ago • Fabian Grammes

Hi, In single-end mode, does feature counts use the the template length (col9 in sam file) to check for an overlap with the feature, or the read length? I have paired-end data with no unmated...reads, I allow multimatchs, so I would have assume that feature count use the template length, my count in in single-end mode should be exactly twice than my count in paired-end, but it does not seems to…

featurecounts rsubread

updated 10.7 years ago • samuel collombet

columns = c("GENEID", "SEQNAME")) %>% set_names(c("ID", "Chromosome")) head(gene_annot) rowData(sce) <- merge(rowData(sce), gene_annot, by.= "ID", sort=FALSE) Error in .local(x, ..., value = value) : 26554

error SingleCell annotate

updated 2.8 years ago • sandra.garces.19

div class="preformatted">Hi all, I wanted to test for chromosomal region enriched for my list of DE genes. I tried with the ChrMapHyperGParams but it looks like that just Human...solution to this, the simplest possible question would be if my D.E. genes are enriched in sexual chromosomes vs. autosomes. Is there a better approach than a chisq.test? Thanks, paolo > temp.params &lt…

GO Organism drosophila2 GO Organism drosophila2

updated 16.6 years ago • Paolo Innocenti

chr1 12612 12721 uc001aaa.3 chr1 13220 14409 I also have coordinate of copy number data like this Chromosome Start End Segment_mean Num_prob 1 64613 5707515 0.981113452 1 5712940 5732322 0.981113452...0.981113452 I want to calculate how many exon locate in the segment position, potentially the number of exon …

genomicrange intersect

updated 5.8 years ago • Fereshteh

expression analysis between them with RNA-seq? Expression is going to be confounded with the number of chromosome copies. Thanks, &nbsp

ploidy normalization rna-seq differential expression assumption

updated 8.8 years ago • aec

library(org.Mm.eg.db) library(org.Rn.eg.db) library(magrittr) # Return the number of genes on chromosome 'chr' number_of_genes_on_chromosome <- function(chr, gene_id_to_chromosome) { gene_id_to_chromosome...gt;% toTable %>% filter(chromosome == chr) %>% nrow } # Return a table counting the number of…

org.hs.eg.db gene ontology mitochondria

updated 8.2 years ago • Owen Dando

Dear group, In GOvis.pdf , vignette for GOstats on page 7, code snippet for representing a pie-chart there are some objects that are difficult to guess their origin. I request if any one can suggest how they can be created

GOstats GOstats

updated 18.0 years ago • Srinivas Iyyer

<div class="preformatted"> I'm in search of copy number analysis implementation that would fit for Hadoop/Mapreduce paradigm; I appreciate if anyone has used/experienced with copy number analysis that can be used with Hadoop/Mapreduce and point me to those. Hadoop is a software framework on Linux that allows...div class="preformatted"> I'm in search of copy number analysis implementatio…

updated 13.8 years ago • mcoyne@boninc.com

preformatted">Hi, Given a set of entrez IDs, I wanted to know their start and end locations on the chromosome. I am using biomaRt, but get the following error: ------------------------------------------- > entrezID = "7471" > getBM(attributes = c('hgnc_symbol','chromosome_name

GO biomaRt GO biomaRt

updated 16.5 years ago • Tim Smith

that has a very large (negative) t-statistic. Section 13.2.4 suggests using gene sets defined by chromosome bands to do the same analysis. I have found an "interesting" chromosome band (cytogenetic) location, and I would like

Pathways hgu95av2 Pathways hgu95av2

updated 17.2 years ago • McGee, Monnie

<div class="preformatted">Hi Bioconductors, Download numbers for Bioconductor Software packages are online at: http://bioconductor.org/packages/stats/ There is no by-version or...div class="preformatted">Hi Bioconductors, Download numbers for Bioconductor Software packages are online at: http://bioconductor.org/packages/stats/ There is no by-version

Cancer Cancer

updated 17.1 years ago • Hervé Pagès

Hi, For the Affy 6.0 platform, I would like to know the default tool for obtaining copy number estimates prior to smoothing across loci (raw copy number). If CNAT is the default, is there a command-line version of this

affy affy

updated 17.4 years ago • Rob Scharpf

m using CHARM packages for the analysis of differentially methylated regions. I can have a list of chromosomal locations indicating genes but I don't know how I map this location into specific gene names. > head(pns) [1] "chr19

Lung charm genomes Lung charm genomes

updated 13.5 years ago • Yoo, Seungyeul

Dear all, I have bed files with ChIP-seq data, with sequence (chromosome) names like this: chr1, chr10, chr11, chr12, chr13, chr13\_random, chr14, . . ., chrX I  import the bed file data into a DiffBind...Dear all, I have bed files with ChIP-seq data, with sequence (chromosome) names like this: chr1, chr10, chr11, chr12, chr13, chr13\_random, chr14, . . ., chrX I  import t…

DiffBind ChIP-Seq

updated 11.1 years ago • Georg Otto

ERscores and ERregions (from MAT scores and Protein Enriched region functions). One outputs just the chromosome number, and the other outputs chr and the number. So for ERscores it looks like chr1 . . . chr2 . . . And for ERregions it looks

updated 14.5 years ago • Jillian Rowe

div class="preformatted"> Dear All In regards to GenomeGraphs, is there a maximum number of transcripts per gene allowed? Amanda Miotto a.miotto at griffith.edu.au Software Engineer. Research Computing

GenomeGraphs GenomeGraphs

updated 17.4 years ago • Amanda Miotto

suggestions that will allow me to take advantage a the large amount of bacterial genomic data for homology studies? Thank you for your help. Noah Attempted Solution (for a single genome): > bacGenome = useMart("bacterial_mart_7...filters, values = values, : The query to the BioMart webservice returned an invalid result: the number of columns in the result table does not equal the nu…

Alignment biomaRt genomes Alignment biomaRt genomes

updated 15.1 years ago • Noah Dowell

recombination generates novel combinations of genetic variation via reciprocal exchange between homologous chromosomes. To better understand this process we are generating genome-wide recombination frequency maps

Genetics Arabidopsis thaliana PROcess Genetics Arabidopsis thaliana PROcess

updated 14.9 years ago • Krys Kelly

I've tried to compare the output from Cellranger 3.0 with DropletUtils::emptyDrops() in term of number of cell-containing droplets. The web-summary from the Cellranger run outputs 1240 cells which is indeed very consistant...of the curve is around the 1100-1300th barcode). It is far less than I expected with regard to the number of cells I've put as input but this could be explain by some technic…

CellBarcode DropletUtils emptyDrops() Cellranger scRNAseq

updated 3.9 years ago • gregoire.destreel

I often need to retrieve number of samples or features of a given ExpressionSet. I use constructs like `dim(es)[[2]]`, and just to make my code easier to read

expressionSet

updated 5.7 years ago • aush

and want to use DESeq2 to normalize the counts. However, I used Picrust to correct the 16S copy number for OTUs and the number generated by this correction are not integers (but decimals). Can I used DESeq2 to normalized...my count data (using size factor) obtained by this 16S number correction considering that the DESeq2 was developed based in counts and not in counts corrected by 16S copy number

DESeq2 DESeq2

updated 11.7 years ago • Manoeli Lupatini

Hi, I use RUVSeq and I find it extremely helpful.  I have a question concerning the number of covariables to be used under RUVr. I've realized that increasing the number of covariables makes the groups I want...to see on the PCA more visible and distinct from each other. It follows the the number of DE genes also increases with k. In one of my projects I have 72 samples a…

rnaseq ruvseq RUVr edgeR

updated 10.1 years ago • David Rengel

samples and 8 tumour samples of cancer patients. The average coverage of CpGs on the considered chromosome (for example, 7th chromosome) is 2.4 (from 0.4 to 4.6 in different samples). Number of CpGs in this chromosome is 1 247...716, Number of CpGs which are covered by at least 1 read in all 16 samples is  18 543, Number of CpGs with 0 coverage in all samples...is 0... …

bsseq R package

updated 8.6 years ago • Maria

Dear All, I have some problems running my script with the latest version of ChIPQC1.12. The script was working well on the older version of the package. I was wondering if someone else is also facing the same problem and could give me a solution. Below is my code and output: <pre> samples = read.csv("metadata.csv") mydata= ChIPQC(samples, annotation=NULL, chromosomes=NULL)<…

chipqc R

updated 8.5 years ago • tuteja.reetu

hierarchy generated in OpenCyto. My problem is that I can't seem to find a way to control the number of decimals in gate labels. Default seem to be 3 numbers from the first non-zero number. Thus, in a gate the geom\_stats label

ggcyto

updated 9.1 years ago • anders.tondell

where one probeset seems to be annotated to multiple positions in the same general area of a single chromosome. See below for details. Thanks in advance, Neil Hayes using R - 1.9.0 geneplotter 1.4.0 hgu95av2 1.5.1 (downloaded...package to generate an object of class "chromLocation" for the 95av2 chip. Next I extracted the chromosome locations as below: chrObj <- buildChromLocation("hgu…

Annotation geneplotter affy Annotation geneplotter affy

updated 21.6 years ago • david neil hayes

fast5files) Checking file validity Reading Channel Data Reading Raw Data Reading Template Data Reading Complement Data Reading Template FASTQ Error in .subset(x, j) : invalid subscript type 'closure'   R 3.3.1

IONiseR

updated 9.3 years ago • kaganr

the data. Using the function depmap_copyNumer() results in the wrong table…not getting the copy number data…I think it is the metadata table…so maybe wrong linked. Cheers, Danny

software error depmap

updated 4.7 years ago • DannyM

textural descriptions of the corresponding genes org.Sc.sgdENSEMBL Map Ensembl gene accession numbers with SGD Gene identifiers org.Sc.sgdENSEMBLPROT Map Ensembl protein acession numbers with SGD Gene identifiers...org.Sc.sgdENSEMBLTRANS Map Ensembl transcript acession numbers with SGD Gene identifiers org.Sc.sgdENTREZID Map Systematic ORF identifiers with Entrez Gene identifiers org…

org.Sc.sgd.db

updated 2.1 years ago • Chih

filters=c("snp_filter"), values=( "rs6171921" ), mart = snpmart)->sps Variation Name Chromosome name Position on Chromosome (bp) Variant Alleles C57BL/6J CAST/EiJ 1 rs6171921 2 157329549 G/A G A Error in getBM(attributes...chr_name", "chrom_start", : The query to the BioMart webservice returned an invalid result: the number of columns …

SNP biomaRt SNP biomaRt

updated 13.0 years ago • Christopher T Gregg

Bioconductor. Now, I want to add a column in the final output, which includes the gene accession number of reference sequence, for example, NM_008725 besides gene entrez ID and gene name. In this way, I could match probe ID...to their corresponding accession number. But how can I write a code to implement it? Thanks in advance. YiSong PS. library("annotate"); library("mouse4302.db"); tota…

probe limma probe limma

updated 15.4 years ago • Yisong Zhen

Dear list, I am using snapCGH to look at Agilent's mouse aCGH array. my MAlist object (MA1) have chromosomes 1-19, 23 and 24. After I run the processCGH function, chromosome 23 and 24 are no longer in my new MAlist object (MA2

aCGH Survival Cancer annotate genefilter affy DNAcopy aCGH GLAD tilingArray snapCGH

updated 18.3 years ago • caiwei@mdanderson.org

web site, it seems to me that Affy's Mapping 500K Array Set SNP chips do not probe the p arms of chromosomes 13, 14, 15 and 22. Is that right? If so, does anyone know why that is? Thanks in advance. -Ben The information transmitted

SNP affy SNP affy

updated 18.3 years ago • Wittner, Ben

strata, ...) : One or more of the strata contain less than 42 elements. Please reduce the number of strata so that there is enough in each stratum. using my own data, I got the error above. I finally got around the error...patient (with a total 853 patients in the dataset). Consequently, it is not possible to run a huge number of controls, given the number of experimental cells per slide. O…

Normalization vsn Normalization vsn

updated 15.8 years ago • Eric E. Snyder

div class="preformatted">Hi, I am trying to create a redundant list from two different lists of chromosomal ranges as follow: *List 1:* Chr Start Stop chr1 0 98595 chr1 17012368 17012439 chr1 17017304 17029919 chr1 17246620

updated 13.8 years ago • Yadav Sapkota

If I search UCSC for A3GALT2 I get the following location chr1:33,772,365-33,778,183 Why are the chromosomal locations for this probe different? Chris </div

probe probe

updated 13.0 years ago • Fenton Christopher Graham

find DE genes. But I do not understand why even when the bam files and references are the same the number of genes are different in the result of cuffdiff and HTseq. Actually I expected to have different number of counts for...each gene but not getting more (nearly 100) number of genes in HTseq comparing to cuffdiff. Thank you in advance</div

updated 13.1 years ago • Fatemehsadat Seyednasrollah

all, if I understand correctly, the locations as in the affychipidCHRLOC environments are given as chromosome number and base pair. How do I interpret negative values in the slot? Greetings Johannes -- Johannes H?sing There is

updated 22.2 years ago • Johannes Hüsing

It would be great if the organism packages had a templated minimal vignette that included printing out the keytypes and columns. http://bioconductor.org/packages/Homo.sapiens

homo.sapiens organismdbi

updated 8.9 years ago • Michael Love

1594 peaks are identified when the .bam files do not have the 'chr' string in the first column for chromosome name, but the .bed files with the peaks do have the 'chr' string and the number. When I run the analysis with no 'chr' string...I guess it doesn't work. Even the FRiP value is generated for each peakset both when .bam and .bed chromosome columns are mismatched (.bed with 'chr'+number …

diffbind chip-seq

updated 9.3 years ago • D.Hemerich

how to obtain the download number of a Bioconductor package quickly, instead of summing the download number per years in the stat webpage? just like a...bioconductor.org/packages/stats/bioc/DESeq2/DESeq2_stats.tab` could be used to calculate the total number. Seems no API did this sum. added: `https://github.com/r-hub/cranlogs.app/issues/43

badges

updated 3.5 years ago • zhilongjia

Sorry for the stupid question, I'm totally a baginner in cDNA data Analysis... Can I derive the number of wells in a plate from a .gpr file ? I would like to use it for the normalization... I looked in the web and in the mailing list

Normalization Normalization

updated 19.8 years ago • Giulio Di Giovanni

Hi all, I am using fastMMN for batch correction and subsequently buildSNNGraph and cluster\_walktrap for clustering on single-cell rna seq data on multiple samples. However, I end up with way higher number of clusters compared to what I would expect. By setting the steps parameter in cluster\_walktrap it is possible to change...for clustering on single-cell rna seq data on multiple samples. Howe…

scran buildsnngraph cluster_walktrap single-cell

updated 7.4 years ago • tobi

Is there an R module that does NTP? Hoshida 2010 refers to R code that is part of GenePattern, but I'd rather not deal with the admin headaches of setting up a GenePattern server, and I prefer that all my analyses are self-contained anyway. Are there any packages that do this yet? Should I just download GenePattern, find the R code in question, and adapt it to my needs? Thanks -Ed

updated 12.7 years ago • Siefker, Ed B.

ws,nit=10,nrit=1,empty_bins=TRUE,rank=FALSE) Reading bam alignment Q97-k4_filter.bam Total number of imported short reads: 13592073 Extending reads... Creating GRange Object... Extract unique regions... Number of unique...short reads: 13592073 Loading chromosome lengths for BSgenome.Rnorvegicus.UCSC.rn5... Calculating genomic coordinates...Error in vector(length = supersi...ze_chr[length(chromoso…

Alignment BSgenome BSgenome MEDIPS Alignment BSgenome BSgenome MEDIPS

updated 12.3 years ago • Guest User

and change col.names cnvMatrix <-cnvMatrix[,-6] colnames(cnvMatrix) <- c( "Sample.Name", "Chromosome", "Start", "End", "Num.of.Markers", "Aberration") # Substitute Chromosomes "X" and "Y" with "23" and "24" xidx <- which(cnvMatrix$Chromosome...X") yidx <- which(cnvMatrix$Chromosome=="Y") cnvMatrix[xidx,"Chromosome"] <- 23 cnvMatrix[yidx,"…

memory problem gaia

updated 8.1 years ago • drusmanbashir

peak names are in the first column, peak positions  are in the second/third/forth colums (chromosome, start, end) and  normalized number of reads for each sample are in subsequent columns. Regards Konstantin

diffbind read counts extract data

updated 7.7 years ago • k.panov