Bioconductor Forum

wewolski • 10

2 hours ago

Zurich

For : Why does limma contrast.fit produces NA's for all contrast although missing data only in one condition?

efratsh • 0

1 day ago

For : Unable to install packages

ilysR • 0

7 days ago

For : biomaRT connexion problem make failed my unit tests

Sophie Marion de Proce • 0

21 hours ago

University of Edinburgh

For : Cannot install xps package, Mac OS 10.11, R 3.3

jol.espinoz • 30

2 days ago

For : WGCNA: What is `soft thresholding`?

jol.espinoz • 30

2 days ago

For : WGCNA: What is `soft thresholding`?

jma1991 • 40

1 hour ago

For : Reads mistakenly being assigned to Unassigned_NoFeatures category when using featureCounts

jma1991 • 40

1 hour ago

For : Memory-efficient method to calculate GC content of millions of GRanges

hwu12 • 10

10 days ago

For : featureCounts for multiple features

hwu12 • 10

10 days ago

For : Thermo Xcalibur RAW data to MGF

svlachavas • 770

9 days ago

Germany/Heidelberg/German Cancer Resear…

For : Install older specific version from an R package that is on the Bioconductor Repository

reubenmcgregor88 • 0

11 days ago

For : MA plot DiffBind in ggplot2

daw277 • 0

12 days ago

For : maSigPro see.genes function gives "invalid 'times' argument" error for single time course data

Andy91 • 60

14 days ago

Netherlands

For : Understanding contrasts limma

Andy91 • 60

14 days ago

Netherlands

For : Understanding contrasts limma

enricoferrero • 570

14 hours ago

Switzerland

For : Can't upgrade to Bioconductor 3.3?

enricoferrero • 570

14 hours ago

Switzerland

For : How to properly sort GRanges?

enricoferrero • 570

14 hours ago

Switzerland

For : [GenomicRanges] subsetByOverlaps to keep info from both GRanges objects?

charles.foster • 100

14 days ago

For : WGCNA sample size minimum: why?

YunYun • 70

1 day ago

For : it paused in line **byte-compile and prepare package for lazy loading** when install package EnsDb.Hsapiens.v75

YunYun • 70

1 day ago

For : it paused in line **byte-compile and prepare package for lazy loading** when install package EnsDb.Hsapiens.v75

YunYun • 70

1 day ago

For : it paused in line **byte-compile and prepare package for lazy loading** when install package EnsDb.Hsapiens.v75

alexandr.gopanenko • 20

3 days ago

For : Problem with systemPipeR package: run_edgeR or run_DESeq2 functions don't work

Batool • 370

17 minutes ago

For : Comment: `ggbio` package can't be installed

Batool • 370

17 minutes ago

For : Comment: `TxDb.Hsapiens.UCSC.hg19.knownGene` and `Homo.sapiens` can't be installed anymor

Batool • 370

17 minutes ago

For : `TxDb.Hsapiens.UCSC.hg19.knownGene` and `EnsDb.Hsapiens.v75` can't be installed anymore

Batool • 370

17 minutes ago

For : Comment: `ggbio` package can't be installed

Batool • 370

17 minutes ago

For : `ggbio` package can't be loaded

Batool • 370

17 minutes ago

For : Comment: it paused in line **byte-compile and prepare package for lazy loading** when in

Batool • 370

17 minutes ago

For : `TxDb.Hsapiens.UCSC.hg19.knownGene` and `EnsDb.Hsapiens.v75` can't be installed anymore

Batool • 370

17 minutes ago

For : `ggbio` package can't be loaded

Batool • 370

17 minutes ago

For : Comment: `ggbio` package can't be installed

Batool • 370

17 minutes ago

For : Comment: `TxDb.Hsapiens.UCSC.hg19.knownGene` and `Homo.sapiens` can't be installed anymor

Batool • 370

17 minutes ago

For : Comment: `ggbio` package can't be installed

Batool • 370

17 minutes ago

For : Comment: it paused in line **byte-compile and prepare package for lazy loading** when in

Batool • 370

17 minutes ago

For : `TxDb.Hsapiens.UCSC.hg19.knownGene` and `EnsDb.Hsapiens.v75` can't be installed anymore

Batool • 370

17 minutes ago

For : `ggbio` package can't be loaded

Guido Hooiveld ♦ 2.8k

3 hours ago

Wageningen University, Wageningen, the …

For : Ensembl plants at annotationHub?

knholm • 0

21 days ago

For : pointSize, labSize, and DrawConnectors error when plotting EnhancedVolcano

Nik Tuzov • 70

22 days ago

United States

For : Normalization methodology in DESeq/DESeq2 vs edgeR

abf • 30

15 days ago

For : A: Unexpected error with topGO, cannot build topGOdata object

abf • 30

15 days ago

For : A: Unexpected error with topGO, cannot build topGOdata object

heikki.sarin • 0

27 days ago

For : DESeq2 model - How to test case/control time course model when taking account within sample variability?

Thomas Girke ♦ 1.7k

4 weeks ago

United States

For : A: heatmap.2() get matrix after hierarchical clustering

Jenny Drnevich ♦ 2.0k

4 weeks ago

United States

For : trouble using select() to get all GO terms when have duplicate query IDs

Jenny Drnevich ♦ 2.0k

4 weeks ago

United States

For : Problem with tximport(reader = read_tsv) and workaround

svlachavas • 770

9 days ago

Germany/Heidelberg/German Cancer Resear…

For : Error in PCA analysis and with ggbiplot function

Cale Reid • 10

4 weeks ago

San Francisco, CA

For : Adjusted p-value output from Limma different from output using p.adjust?

anamaria • 10

20 days ago

Barcelona, Spain

For : A: How to use ENCprime via coRdon with a custom background sequence set?

L_K • 0

25 days ago

For : Age covariate continuous vs. categorical

L_K • 0

25 days ago

For : Applying SVA to RNA-Seq dataset

georgia.katsoula • 10

20 hours ago

For : ah <- AnnotationHub() Error in UseMethod("filter_"): no applicable method for 'filter_' applied to an object of class "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')"

anton.kratz • 60

6 weeks ago

United States, San Diego, UCSD

For : [sva] Error in density.default(x, adjust = adj) : 'x' contains missing values

ijvechetti • 0

6 weeks ago

For : DESeq2 for multiple groups

Qiang • 70

5 weeks ago

For : Error in parseURI("") : cannot parse URI (rtracklayer package)

Freddie • 10

6 weeks ago

UCL

For : msa compilation failure - multiple definition of `GC_jmp_buf' in gc-7.2

Mthabisi Moyo • 30

25 days ago

For : ensDbFromGtf error from gtf file downloaded from GENCODE.

rodrigo.duarte88 • 30

6 weeks ago

For : A: How to run the annotation tool for GARFIELD v2: garfield_annotate_uk10k.sh

Bogdan • 610

16 days ago

Palo Alto, CA, USA

For : extracting the genes associated with the clusters

Gordon Smyth 41k

1 hour ago

WEHI, Melbourne, Australia

For : A: Possible ways of performing differential gene expression and analysis of RNA-Seq

ATpoint • 390

1 hour ago

Germany

For : Comment: Normalise to a housekeeping gene in DESEq2

ATpoint • 390

1 hour ago

Germany

For : Comment: Normalise to a housekeeping gene in DESEq2

svlachavas • 770

9 days ago

Germany/Heidelberg/German Cancer Resear…

For : Error using function NbClust regarding multiple values in the argument "index" of package NbClust for getting the optimal number of clusters of a dataset

mscherer • 40

2 hours ago

For : A: RnBeads::combine() - error?

biomiha • 20

9 weeks ago

UK/Cambridge

For : Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array extent

shangguandong1996 • 20

1 hour ago

For : Can I completely repeat the DiffBind results using DESeq2?

shangguandong1996 • 20

1 hour ago

For : how to get the estimated libSize in DiffBind

DataFanatic • 0

9 weeks ago

For : Adjusting batch effects in microarray expression data using empirical Bayes methods

Konstantin Okonechnikov • 20

9 weeks ago

For : DESeq2: one condition vs multiple combined

Konstantin Okonechnikov • 20

9 weeks ago

For : Integrating the computed spike-in coefficients for the normalisation before differential peaks analysis

GFM • 20

29 days ago

European Union

For : DiffBind with highly variable FRiP (Fraction Reads in Peaks)

Catalina Aguilar Hurtado • 60

9 weeks ago

United States

For : Heatmap from DESeq2 DE genes

Catalina Aguilar Hurtado • 60

9 weeks ago

United States

For : Heatmap from DESeq2 DE genes

Frédéric Crémazy • 0

8 weeks ago

Paris

For : How to generate custom annotation for rat genome rn6 in ChIPQC

Johannes Rainer ♦ 1.8k

3 days ago

Italy

For : A: How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi

ycding • 10

9 weeks ago

United States

For : how to analyze TCGA CNV data

igor • 40

28 days ago

United States

For : DiffBind for ATAC-seq

hamza_karakurt • 50

7 weeks ago

For : Differential Expression Analysis between conditions of single cell RNA-Seq

Tim Peters • 120

10 weeks ago

Australia

For : Issue with SummarizedExperiment thru DSS::makeBSseqData

Jonathan Göke • 20

4 days ago

Singapore

For : Answer: proActiv: No major promoter when internal promoters are strong

yueli7 • 10

23 days ago

China

For : install RCurl in R

mmfansler • 30

7 weeks ago

MSKCC | New York, NY

For : A: How do I subset a GRanges object based on chromosome (and approximate region)?

ramiro.barrantes • 10

8 weeks ago

United States

For : DESeq2 results are completely different for the same contrast when considering different designs

Yunshun Chen • 690

10 days ago

Australia

For : C: Appropriate use of the function treat of the limma package

Wolfgang Huber 13k

3 days ago

EMBL European Molecular Biology Laborat…

For : exprs function - clash with dplyr

maleknias • 0

4 weeks ago

For : Find DEPs among TMT labeling proteom time course data by limma

nick.eagles • 90

15 days ago

For : Answer: Changing Row Names of MultiAssayExperiment Assay

nick.eagles • 90

15 days ago

For : Answer: Changing Row Names of MultiAssayExperiment Assay

maleknias • 0

4 weeks ago

For : NA values of count matrix in class DESeqDataSet

jiazhou0116 • 0

11 weeks ago

For : Error in Forge the target package (BSgenome)

atakanekiz • 30

9 weeks ago

For : Understanding clusterprofiler enrichment results

m.metsger • 0

11 weeks ago

For : tximport abundanceCol parameter not functioning for rsem data

dagurim • 0

11 weeks ago

For : DESeq2: Model matrix problem with 30 samples

inzirio • 10

11 weeks ago

For : SingleR Error in getMethod(generic, "ANY")

Assa Yeroslaviz ♦ 1.5k

5 weeks ago

Munich, Germany

For : A: Problem with biomart's listMarts function

Assa Yeroslaviz ♦ 1.5k

5 weeks ago

Munich, Germany

For : A: could not find symbol "keepNA" in environment of the generic function

Assa Yeroslaviz ♦ 1.5k

5 weeks ago

Munich, Germany

For : DESeq2 produces adjusted p-values = 1

Kevin Ushey • 10

11 weeks ago

United States

For : Recommended way to use BiocInstaller / BiocManager in packages on CRAN?

Do it! • 0

6 weeks ago

Germany, München

For : correlation analysis

pkachroo • 10

11 weeks ago

For : Do I have clustering by library size?

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