Bioconductor Forum

p/93932/> (Differential binding of ATAC-seq data with no replicates) And the paper "_De novo_ detection of differentially bound regions for ChIP-seq data using peaks and windows: controlling error...rates correctly": https://academic.oup.com/nar/article/42/11/e95/1442937  "This paper provides some recommendations to maintain error control for _de novo_&am…

atac-seq sample size Peak Normalize

updated 7.9 years ago • jaime.alvarez.benayas

include the results of running the following in an R session sessionInfo( ) R version 4.1.2 (2021-11-01) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 22000

analsyis WGCNA

updated 3.7 years ago • Afsana

I am having trouble understanding the workflow described[ in the paper](http://f1000research.com/articles/3-95/v2). I have a data set of four fastq files from a crispr/cas9 screening experiment...samples and two __treated__ samples. I am not sure how to use the workflow described in the paper and the R vignette to analyze my data. I have read both the paper and the vignette, but I still…

edger sgrna processamplicons

updated 7.7 years ago • Assa Yeroslaviz

In the [this metagene paper][1], the distance in the plot is shown in base-pair, but in the current metagene2, the distance is showed in bins. There is where

metagene metagene2

updated 3.1 years ago • sfpacman

div class="preformatted">Hi The spotSegmentation paper in bioinformatics was a pretty good read, but after downloading the r package, I still can't figure out how to get my tiff

spotSegmentation spotSegmentation

updated 20.4 years ago • michael watson IAH-C

Hi, I'm learning GSVA paper recently and I'm wondering why GSVA chose Si/4 as the bandwidth for a Gaussian kenel estimation. I have read all the document

GSVA gsva

updated 7.8 years ago • Xingyu

fora``` by semantic similarity. My ultimate goal is to obtain a figure like Figure 3 in the ViSEAGO paper. With kind regards Tim

ViSEAGO

updated 4.7 years ago • tim.meese

of data of the DESeq2 function normalises raw counts. Can anyone give me a reference to a paper where this has been described? I have not been able to find anything yet, unfortunately. Thank you so much, Bine

DESeq2

updated 4.8 years ago • Bine

Recently I read one of your paper titled with “FELLA: an R package to enrich metabolomics data”, and met a problem. I want to present the results of network

software error FELLA

updated 6.9 years ago • jnzd_hemaozhang

binomial distribution of each gene count_ K\_ij_ are computed.  ## Information given in the paper from from Love, Huber, Anders (2010) In the paper (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014...j.  _q\_ij_ is modeled as _log q\_ij = sum (x\_jr \* beta\_ir)_ ## My questions In the paper they say they start by fitting a negative binomial GLM to the ge…

deseq2 design matrix

updated 6.9 years ago • nikosbosse

and counts. Gordon Smyth has written that TPMs should not be used as input to EdgeR. In a recent paper (F1000 Research 2016,4:1521) Soneson, Love, and Robinson have presented evidence that the method they call simplesum_avextl...is as good or better for differential expression than alignment+featureCounts. In a comment on that paper, Lior Pachter advocates simply adding the reads assigned to ea…

RNASeq-quantification edgeR TPM

updated 6.8 years ago • raf4

Hi, In most of the chipseq papers, inorder to visualize the intensity signals the data is represented in the form of normalized counts. One such is this...paper http://www.nature.com/nature/journal/v488/n7409/full/nature11243.html, in the supplementary methods they described

chipseq bioconductor

updated 10.2 years ago • ngs06

are Agilent 244k, Affy SNP 6.0, Illumina 1M. I have looked in the recent nature and nature genetics papers where 76 - 27 % of the CNVs detected by a fosmid approach (Mapping and sequencing of structural variation from eight human...analysis of SNPs and copy number variation). The sensitivity of Illumina 1M was 47% in another paper (Systematic assessment of copy number variant detection via geno…

SNP Genetics Coverage CGH affy SNP Genetics Coverage CGH affy

updated 17.0 years ago • Johan Lindberg

<div class="preformatted">Dear all, I am now working on some time-course experiments and I have applied to them some classical statistic methods to identify genes that change their expression between time points. However I have read few papers (such as Peddada et al. Gene selection and clustering for time-course and dose?response microarray experiments using order-restricted inference; GUO…

Microarray Clustering Microarray Clustering

updated 22.2 years ago • edoardo missiaglia

mirrors.tuna.tsinghua.edu.cn/CRAN/ Bioconductor version 3.12 (BiocManager 1.30.15), R 4.0.5 (2021-03-31) Installing package(s) 'org.Hs.eg.db' installing the source package ‘org.Hs.eg.db’ 试开URL’https://bioconductor.org

AnnotationDbi org.Hs.eg

updated 4.5 years ago • 1065463017

BiocManager::install('traviz', force=T) Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01) Installing package(s) 'traviz' trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/traviz_1.0.0.tar.gz...installation of package ‘traviz’ had non-zero exit status sessionInfo( ) R version 4.1.2 (2021-11-01) Platform: x86_64-conda-linux-gnu (64-bit) Running under…

traviz

updated 3.9 years ago • gennady.margolin

Would you like to tell me whether DESeq2 can analyze m6A-seq to detect differential m6A peaks? Other papers firstly used input reads to normalize m6A-seq reads, and then performed fisher’s exact test. It seems that DESeq2 can

DESeq2 MeRIP-seq

updated 4.0 years ago • BioEpi

Within the paper *Workflow for Microbiome Data Analysis: from raw reads to community analyses* under the header construct phylogenetic

phyloseq

updated 4.5 years ago • klltnq

if there is any sample swap? Could any one please give me any idea how to do this, or recommend any papers or software? Thanks in advance

WES

updated 9.1 years ago • Haiying.Kong

wonder how i can compare my results with signatures listed by the Sanger Institute (Figure 2 in the paper below)? Signatures of mutational processes in human cancer <http://www.nature.com/nature/journal/v500/n7463/full/nature12477.html

somaticsignatures

updated 9.1 years ago • jonessara770

A recent paper in the journal RNA by [Schurch et al](http://rnajournal.cshlp.org/content/early/2016/03/30/rna.053959.115?top=1) had reported...e.g. p-value = 0. The authors have been very responsive and quick in helping to correct the paper and figures. Furthermore, I could easily try to replicate their analysis using their publicly available processed...data (htseq-count files) and could look o…

deseq2

updated 9.6 years ago • Michael Love

I am having trouble understanding the workflow described[ in the paper](http://f1000research.com/articles/3-95/v2). I have a data set of four fastq files from a crispr/cas9 screening experiment...and two __treated__ samples. I am not sure how to use the workflow described in the paper and the R vignette to analyze my data. I have read both the paper and the vignette, b…

edger processamplicons sgrna crispr

updated 4.7 years ago • Assa Yeroslaviz

are normally too small for any meaningful statistics, but I need to conduct a PCA in R for a paper I'm writing. I'm using the pcaMethods package (method=ppca) because my dataset has a lot of non-random missing data and chatGPT...scale than my primary x and y-axis. I've included a picture below to illustrate. I've looked in a paper published under my advisor several years ago and the PCA performed…

pcaMethods pca

updated 22 months ago • yousavdj

div class="preformatted">Hi all, I just recently came across a paper by Dai et al, Nucleic Acids Research, 2005 that talks about transcript definitions of the GeneChip arrays being based...builds. They have in turn reannotated the platforms based on specific critieria outlined in the paper. Has anyone tried their custom CDFs? Also, how would one patch this to use with gcrma? Best regards,…

Genetics Cancer Genetics Cancer

updated 19.2 years ago • Lo, Ken

Hello I am new to the analysis of bisulfite sequencing data with edgeR. I read the user guide and wrote code to perform the analysis. With this post, I want to check if my design matrix and contrasts are the correct ones to assess the question of interest. ``` target sample subject condition 1 SampleA animal1 normal 2 SampleB animal1 treated 3 SampleC animal2 normal 4 Sampl…

edger bisulfite sequencing

updated 5.5 years ago • tim.meese

to create a citation for [edgeR user manual][1] ? I wasn't sure whether to cite the original edgeR paper or if the user manual needs a separate citation? Thanks [1]: https://www.bioconductor.org/packages/devel/bioc/vignettes

edgeR

updated 19 months ago • k___

have GOMiner and GOstats functional, is cool Is there any serious reason to use one or the other? Paper in Nucleic Acids Research 2008 by Al-Shahrour say GOMiner cited 408 times GOstats cited 249 times [[alternative HTML

GOstats GOstats

updated 15.6 years ago • Loren Engrav

calculate the differentially expressed genes. Of course, the results are not identical. I read many papers, and both of the packages are evaluated quite good. My question is, what I can do? Is that possible I can get the intersection

edger deseq2

updated 7.6 years ago • yueli7

Hi, I did RNA-seq analysis and Im planning to analyze with WGCNA, I have seen several papers with trait data, but I have a large RNA-seq sampling but few trait data. I was wondering if it is valid do WGCNA just with

wgcna rnaseq

updated 8.5 years ago • adriana.gallego.02

possible to obtain allele-specific copy numbers using Illumina methylation microarrays (450K)? This paper discusses some approaches used in SNP-array: http://genomebiology.com/content/9/9/R136 Any help will be greatly appreciated

updated 11.6 years ago • Aaerp

Hi all, I am interested in investigating clustering of samples using heatmap.2 in this paper “BioC2014: RNA-Seq workflow for differential gene expression”. However, I find it difficult to explain the Row Z-Score...Hi all, I am interested in investigating clustering of samples using heatmap.2 in this paper “BioC2014: RNA-Seq workflow for differential gene expression”. However, I find it difficul…

deseq2 heatmap.2

updated 7.7 years ago • haitrieuphan82

for meta-analysis of RNAseq experiments. Any ideas pointing towards suitable packages, websites, papers are appreciated. Is there a way to compare microarray data and RNAseq data. I just want to initiate discussion and further

RNAseq meta-analysis microarray public data sets

updated 6.8 years ago • Vladimir Krasikov

service is temporarily down. Trying to fetch the chromosome length data. ``` R version 4.1.0 (2021-05-18) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Big Sur 11.6

Gviz

updated 4.2 years ago • RUser743

Recently I updated my R from 3.6.3 to 4.0.5. I can install packages by BiocManager::install() while I was using R 3.6.3. However, I cannot install packages by BiocManager::install() while I am using R 4.0.5. I can install packages such as ggplot2 by install.packages("ggplot2") in R 4.0.5. I don't know why BiocManager::install() didn't work in my computer for R 4.0.5. Please see the error message …

BiocManager

updated 4.6 years ago • mizzle

Hi everyone, I am one of the contributors of the [MesKit Bioconductor package](https://bioconductor.org/packages/devel/bioc/html/MesKit.html). We made some changes on the MesKit package few days ago and pushed to both the github and Biocondutor repo. However, no changes were found when we checked the Bioconductor landing page of MesKit. Although the latest version could be obtained when usi…

MesKit

updated 4.7 years ago • wangx555

the count matrix is just 3.4GB. Based on my understanding of what `dream()` does (I read [this paper](https://academic.oup.com/bioinformatics/article/37/2/192/5878955)), the modeling procedure for each gene is completely...Any advice would be very much appreciated! # Session Info ```r > sessionInfo() R version 4.0.4 (2021-02-15) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubunt…

BiocParallel limma variancePartition

updated 4.5 years ago • Junghoon

CRAN: https://cran.rstudio.com/ Bioconductor version 3.14 (BiocManager 1.30.19), R 4.1.1 (2021-08-10) Old packages: 'Matrix' Update all/some/none? [a/s/n]: ```r sessionInfo( ) ``` R version 4.1.1 (2021-08-10) Platform: x86_64-apple-darwin17.0

Versions Update BindingSiteFinder

updated 2.9 years ago • M.Klostermann

Mus musculus - release M27 ] useHub=TRUE: checking for TxDb via 'AnnotationHub' snapshotDate(): 2021-05-18 did not find matching TxDb via 'AnnotationHub' building TxDb with 'GenomicFeatures' package Error in makeTxDbFromGFF...the 'format' argument to specify the format ("gff3" or "gtf"). > sessionInfo() R version 4.1.0 (2021-05-18) Platform: x86_64-apple-darwin17.0 (64-bit) Running unde…

tximeta

updated 4.2 years ago • Jag

<div class="preformatted">Dear Sir/Madam, I have read the paper of DESeq, it seems mainly be used for detecting differential expression genes. Could I use the same methods as genes to...div class="preformatted">Dear Sir/Madam, I have read the paper of DESeq, it seems mainly be used for detecting differential expression genes. Could I use the same methods as genes

DESeq DESeq

updated 14.3 years ago • geng chen

that the results obtained by this pipeline are not replicas of the results mentioned in the research paper. I have used the same dataset that was used in this research article. Can you suggest that why my results are different

microarray maEndtoEnd

updated 7.2 years ago • salmatariq080

used in conjunction with Limma to do this? > > Also, I find the Bayesian theory in the paper >by Gordon Smyth ("Linear Models and Empirical >Bayes Methods..." tough going) Can anyone >please recommend a book or...different quantities to be computed compared to full Bayes. I hope that the final formula in the paper make intuitive sense even though the ma…

Bayesian Classification limma bridge Bayesian Classification limma bridge

updated 21.4 years ago • Gordon Smyth

but what about intramodular connectivity vs. kME values? <span style="line-height:1.6">I have seen papers where folks select a hub gene based on it having a high intramodular k (connectivity) value within the module itself...kME) values to pick a hub gene? </span> Discussion of these merits or pointing me to a paper would be most appreciated as I am having trouble finding e…

WGCNA Hub Genes KmE Intramodular Connectivity

updated 10.4 years ago • brohawndg

GOGraph(bpCutLeaves, GOBPPARENTS) > postscript ("bpCutLeavestreeTest.ps", width=100, height = 100, paper="special"); plot (bpCutLeavestree); dev.off() quartz 2 > bpCutLeavestree A graphNEL graph with directed edges Number of...like GO:0000002="red" Then I do > postscript ("bpCutLeavestreeTest.ps", width=100, height = 100, paper="special"); plot (bpCutLeavestree, nodeAtt…

GO graph Rgraphviz GO graph Rgraphviz

updated 18.1 years ago • Loren Engrav

RUV as distinct from NanoStringNorm on this small, one-batch dataset? 2. I have read the recent paper on RUV-III as applied to Nanostring: https://www.ncbi.nlm.nih.gov/pubmed/31114909 Should RUV-III be applied to a differential...as distinct from one in which the factors of interest are unobserved? After reading the paper, I am not clear on this point (my fault). 3. If RUV-III sho…

RUV Nanostring RUV-III

updated 5.6 years ago • raf4

linked transcriptome: [ Ensembl - Danio rerio - release 104 ] loading existing EnsDb created: 2021-11-03 18:43:46 loading existing transcript ranges created: 2021-11-03 18:43:46 Warning message: In checkAssays2Txps(assays...gt; gene_summarized <- summarizeToGene(txi_data) loading existing EnsDb created: 2021-11-03 18:43:46 obtaining transcript-to-gene mapping from database Error: i…

tximeta SummarizedExperiment DESeq2

updated 4.1 years ago • alex.weiss

Hi, I am new to using h5 files. I have some data from some collaborators and while I am able to list the contents using ``` hfls("file.h5") ```, when I try to open the file using ``` h5f = H5Fopen("file.h5") ``` I get the following error Error in H5Fopen("file.h5") : HDF5. File accessibility. Unable to open file. My session info is as follows ``` R version 4.1.2 (2021-1…

hdf5 h5 rhdf5

updated 3.4 years ago • dNand

res = results(dds2,contrast=c("cond","Lib1_Tre",'Lib2_Tre')) sessionInfo( ) R version 4.1.0 (2021-05-18) DESeq2_1.32.0

DESeq2

updated 4.3 years ago • Raj

CRAN: https://cran.rstudio.com/ Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.0 (2021-05-18) Installing package(s) 'blockwiseModules' Old packages: 'cachem', 'RSQLite', 'survival' Update all/some/none? [a/s/n]: n Warning

Bioconductor

updated 4.3 years ago • orchidsinvalley

https://cran.rstudio.com/ Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.0 (2021-05-18) Installing package(s) 'blockwiseModules' Old packages: 'cachem', 'RSQLite', 'survival' Update all/some/none? [a/s/n]: n Warning

Bioconductor

updated 4.3 years ago • orchidsinvalley

gt; > BiocManager::install("DESeq") Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.4 (2021-02-15) Installing package(s) 'DESeq' Installation path not writeable, unable to update packages: survival Warning message

DESeq2

updated 4.7 years ago • Evy_00

from the down stream statistical analysis. This was/is quite a debate. Can anybody point out a paper reviewing this issue? kind regards, Arne</div

updated 21.2 years ago • Arne.Muller@aventis.com

I am trying to rerun the simulation in the CSAW paper, but the autosim.R file (http://bioinf.wehi.edu.au/csaw/autosim.R) does not seem to work. I run autosim.R with the following

csaw

updated 9.2 years ago • endrebak85

<div class="preformatted">Hey Guys Looking for recommended packages/papers to do function enrichment analysis in gene clusters in R/bioc. The specie in my case is Chlamydomonas so would need a...div class="preformatted">Hey Guys Looking for recommended packages/papers to do function enrichment analysis in gene clusters in R/bioc. The specie in my case is Chlamydomonas so would need

Annotation Annotation

updated 13.0 years ago • Abhishek Pratap

Hi, It says in the paper of EGSEA that it only works with RNA-seq. But it uses EL-objects produced by voom as input, and these can now be produced...Hi, It says in the paper of EGSEA that it only works with RNA-seq. But it uses EL-objects produced by voom as input, and these can now be produced from

EGSEA gene set testing vooma limma voom gsea

updated 8.8 years ago • Pekka Kohonen

learning algorithms in microarray domain which require discrete feature space. I'm looking for a paper or any other type of reference dealing with discretization of continuous gene expression data. If somebody is aware

updated 17.6 years ago • Andrej Kastrin

Biology (ECCB '06). The conference is to take place in Eilat, Israel, on September 10-13. Papers -------- See the paper preparation guidelines: [1]http://www.eccb06.org/new_pages/submission/sub_papers.html Workshops &amp

updated 19.8 years ago • Hershel Safer

which is by far the > best I've read. Thank you very much for mentioning this very interesting paper. I don't know why I haven't found it before, I should have, because it deals (almost) exactly with the problem I want to solve...And it sounds really good! The only thing is, that for the method the author describes in his paper, I would also need to build age groups to be able to then com…

GO GO

updated 12.6 years ago • Simone

Hello: I have a rather general question about how and why Bayesian inference have been applied in limma, edgeR, and DESeq1-2.   In the simplest differential expression study there are two regression coefficients, an intercept and slope, the latter also denoted by log fold change. LFC estimates obtained across the features (genes) are quite noisy and are likely to benefit from shrinkag…

limma edger deseq deseq2

updated 8.2 years ago • Nik Tuzov

methylated. Is there a current best practice I could follow? I am struggling to find any recent papers which filter non-variable probes from EPICv2 beta matrices. Thank you for your help! Sasha

DMRcate EPICv2manifest

updated 7 months ago • Sasha

I use MOFA2 to integratively analyse multiple omic datasets. Note the MOFA2 [paper][1] and the MOFA2 [GithHub][2] page. I am wondering if I can extract/calculate uncertainty measures such as confidence intervals

MOFA2

updated 13 months ago • mario_de_manner