Bioconductor Forum

kevin.kingsland ▴ 70

6 years, 2 months ago

DESeq2 with interaction using SVA

heyao ▴ 30

6 years, 4 months ago

scran: Are the log counts expression comparable among different genes within a sample/cell ?

p.janitza ▴ 50

6 years, 6 months ago

Problem installing BiocGenerics

ginggs ▴ 40

6 years, 6 months ago

BiocGenerics built with R 3.4.2 changes behaviour

lpsantamaria ▴ 40

6 years, 7 months ago

biomaRt: error using useDataset or useMart

biakemi ▴ 40

6 years, 10 months ago

readCufflinks problem with extdata

Aaron Lun ★ 28k

6 years, 10 months ago

The city by the bay

Duplicated author affiliations in BiocStyle-based HTML document

Gordon Smyth 50k

6 years, 10 months ago

WEHI, Melbourne, Australia

non-integer counts for edgeR

Michael Love 41k

6 years, 10 months ago

United States

DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)

svlachavas ▴ 830

6 years, 10 months ago

Germany/Heidelberg/German Cancer Resear…

Appropriate use of the function treat of the limma package

svlachavas ▴ 830

6 years, 10 months ago

Germany/Heidelberg/German Cancer Resear…

Preprocessing of Human Gene 2.0 ST microarrays with oligo R package and annotation options

Ryan C. Thompson ★ 7.9k

6 years, 10 months ago

Scripps Research, La Jolla, CA

Can I meaningfully interpret a PCA or MDS plot of data with surrogate variable effects subtracted?

Michael Love 41k

6 years, 10 months ago

United States

recount counts in the example experiment

Keith Hughitt ▴ 180

6 years, 10 months ago

United States

WGCNA: overlapping colors in plotDendroAndColors?

ben ▴ 30

6 years, 10 months ago

DESeqDataSetFromTximport with kallisto abundances.

Biologist ▴ 110

6 years, 10 months ago

How to check the read length for all the TCGA data samples in GDC?

sina.nassiri ▴ 130

6 years, 10 months ago

Switzerland/Lausanne

GSVA indifferent to 'abs.ranking'

j.bergenstrahle ▴ 80

6 years, 10 months ago

Rsubread counting peaks ATACseq

j.bergenstrahle ▴ 80

6 years, 10 months ago

fdrtool - correction of p-values - course found on huber.embl.de

Michael Love 41k

6 years, 11 months ago

United States

Updated DESeq2 performance on highly replicated yeast RNA-seq data

tangming2005 ▴ 190

6 years, 11 months ago

United States

difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto

Johannes Rainer ★ 2.0k

6 years, 11 months ago

Italy

Easy way to sort GRangesList by seqname/start position?

I.Castanho ▴ 50

6 years, 11 months ago

DESeq2 likelihood ratio test (LRT) design - 2 genotypes, 4 time points

JWCarlson ▴ 80

6 years, 11 months ago

DESeqDataSetFromTximport: Error in checkSlotAssignment

dhibar ▴ 60

6 years, 12 months ago

Possible to incorporate the sign or direction of an effect in the IHW covariate?

dmr210 ▴ 30

7 years ago

GC/length bias correction in gene expression quantification - Is CQN necessary if using Salmon --GCBias option?

enricoferrero ▴ 660

7 years ago

Switzerland

Can't upgrade to Bioconductor 3.3?

Johannes Rainer ★ 2.0k

7 years ago

Italy

Problem with biomart's listMarts function

komal.rathi ▴ 120

7 years ago

United States

Extract sequence from DNAStringSet object

deut13 ▴ 80

7 years, 1 month ago

Germany

Error in GRanges: could not find symbol "recursive" in environment of the generic function

Ezgi Karaesmen ▴ 30

7 years, 1 month ago

Gviz: How to control `grid` parameter and how to add horizontal lines with different colors to DataTrack?

Brian Smith ▴ 120

7 years, 2 months ago

United States

Chromosome position to nucleotide - Biostrings?

Ramiro Magno ▴ 100

7 years, 2 months ago

CBMR, Faro, Portugal

[FIXED] Error in Gviz (actually, rtracklayer) | IdeogramTrack

NS ▴ 60

7 years, 2 months ago

United States

Mapping genome regions to gene symbols

fizer ▴ 30

7 years, 2 months ago

US

plotDEXSeq error in plot.window(xlim = c(0, 1), ylim = c(0, max(matr))) : need finite 'ylim' values

Greg Finak ▴ 240

7 years, 3 months ago

United States

An appeal to flow cytometry tools users

kjo ▴ 70

7 years, 3 months ago

What's the deal with biocLite's "Update all/some/none? [a/s/n]"?

John Brothers II ▴ 90

7 years, 4 months ago

Cambridge, MA

Differences between limma voom E values and edgeR cpm values?

Lescai, Francesco ▴ 380

7 years, 7 months ago

Denmark

getBM returns shorter vectors than values

smithng1215 ▴ 30

7 years, 9 months ago

Trouble with Tximport

yi.huang ▴ 30

7 years, 9 months ago

How to remove more than two batches in my data-sets

kmuench ▴ 40

7 years, 11 months ago

United States

What does this error mean? - issue implementing SVA

chris86 ▴ 420

8 years ago

UCL, United Kingdom

Limma camera function never gives any differentially expressed gene sets

Gordon Smyth 50k

8 years ago

WEHI, Melbourne, Australia

BH vs BY in p.adjust + FDR interpretation

andrew.j.skelton73 ▴ 370

8 years ago

United Kingdom

DEXSeq Usage and Expression Confusion

andrew.j.skelton73 ▴ 370

8 years ago

United Kingdom

Plot ggplot2 and ggbio Images Together

cardenasca ▴ 40

8 years ago

Plotting Differentially Methylated Regions

Michael Love 41k

8 years ago

United States

DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)

Jurat Shahidin ▴ 80

8 years ago

Chicago, IL, USA

Find overlap for more than 2 GRanges object simultaneously (reproducible example is updated) ?

Agaz Hussain Wani ▴ 260

8 years ago

India

Annotation package for Codelink 55K Human Array