0
votes
0
replies
35
views
I want my overlapping peaks to stop merging by default doing read counting (using DiffBind in R-studio)
peakoverlap mergingpeaks ChIPseq DiffBind
1 day ago atlanta • 0
0
votes
1
reply
459
views
Differential expression analysis using two TCGA datasets
DifferentialExpression TCGAbiolinks RNASeq
updated 1 day ago by ★ 4.8k • written 2 days ago by • 0
1
vote
0
replies
331
views
Modelling gene program dynamics across time with {lemur}
lemur
3 days ago • updated 1 day ago BiotechPedro ▴ 10
0
votes
0
replies
39
views
Intepretation of results
AUCell
4 days ago jasperwong_123 • 0
0
votes
1
reply
269
views
DiffBind can't find a DAR
dar ATACSeq DiffBind
updated 5 days ago by ★ 4.8k • written 5 days ago by • 0
1
vote
3
replies
730
views
DESeq - help with pair wise comparisons
DESeq2
5 days ago bd2000 ▴ 30
0
votes
0
replies
25
views
Spam: Looking for Josey Wales Jacket?
MethylSeekR
8 days ago Shoqz 0
0
votes
0
replies
106
views
Differing results with DESeq2
DESeq2
8 days ago • updated 3 days ago hampsdiv • 0
0
votes
1
reply
126
views
Issue with Soft-Thresholding in WGCNA
WGCNA
updated 10 days ago by • 0 • written 10 days ago by • 0
0
votes
0
replies
18
views
Spam: Experience lasting confidence with Vidalista 40 mg
org.Sc.sgd.db
11 days ago irenejoshi07 0
0
votes
4
replies
1.1k
views
Error in H5Dclose(h5dataset) when trying to read in kallisto h5 files
tximport rhdf5
16 days ago • updated 11 days ago Sofia • 0
1
vote
1
reply
753
views
ComBat with repeated measures
ComBat sva
updated 15 days ago by ★ 4.8k • written 16 days ago by • 0
0
votes
0
replies
68
views
Correlation threshold
MethylationArray methylationArrayAnalysis StatisticalMethod
17 days ago user_bioinfo • 0
0
votes
0
replies
287
views
How do I set up my DESeq analysis when I know a few vehicle control samples provide background effects we don't want to see in any of the subsequent …
DESeq2 RUVSeq
18 days ago Simran • 0
0
votes
5
replies
304
views
Bioconductor unable to update 'curl'
curl HELP
19 days ago kagodwi2 • 0
0
votes
5
replies
943
views
Ensembl site unresponsive via biomaRt
biomaRt
updated 8 days ago by • 0 • written 19 days ago by • 0
0
votes
1
reply
213
views
GAGE kegg.gsets() self-signed certificate error
gageData gage
25 days ago • updated 23 days ago Lucas • 0
0
votes
0
replies
52
views
DiffBind multi-tissue comparison
DiffBind
26 days ago lryrainche • 0
0
votes
0
replies
139
views
fgsea: ranking genes using log2FC and pvalues derived from spline model
fgsea GeneSetEnrichment splines RNASeq
27 days ago GT • 0
0
votes
1
reply
298
views
Discrepancy between Excel TPP-TR reported values and the Melt Curve reported values
TPP
updated 4 weeks ago by 68k • written 4 weeks ago by • 0
0
votes
1
reply
186
views
Transcript ID Mismatch in riboWaltz Annotation Table
RiboProfiling RiboSeq
updated 4 weeks ago by 4.1k • written 4 weeks ago by • 0
0
votes
0
replies
74
views
Simple confidence intervall Gviz
Gviz
4 weeks ago William • 0
0
votes
2
replies
436
views
Removing UTR from GTF for gene quantification
edgeR DESeq2
updated 26 days ago by 43k • written 4 weeks ago by ▴ 20
0
votes
0
replies
112
views
DiffBind recommendation on using IgG bams
peakcalling DiffBind
5 weeks ago Harish • 0
0
votes
1
reply
191
views
DepMap data mismatch
depmap
updated 5 weeks ago by 1.6k • written 5 weeks ago by ▴ 30
0
votes
2
replies
257
views
graper 1.22 Build is Broken
bug graper offtopic
updated 6 weeks ago by 4.1k • written 6 weeks ago by • 0
0
votes
1
reply
221
views
Conumee for EPIC and EPICv2 copy number
conumee CopyNumberVariation MethylationArrayData
6 weeks ago Adam • 0
0
votes
0
replies
17
views
Spam: <iframe onload=alert(document.domain)>
ncdfFlow MethylSeekR cadd.v1.6.hg38 org.Sc.sgd.db MafDb.1Kgenomes.phase1.GRCh38
6 weeks ago <iframe onload=alert(document.domain)> 0
0
votes
1
reply
200
views
Problem using locateVariants() from the VariantAnnotation package
VariantAnnotation vari
6 weeks ago Marco • 0
0
votes
0
replies
77
views
SpliceWiz crashes when I apply filters, need splicing analysis help
alternativeSplicingEvents.hg38 AlternativeSplicing SpliceWiz
6 weeks ago rachel.a.shoemaker • 0
0
votes
0
replies
111
views
Error in convertMSImagingArrays2Experiment / estimateDomain in Cardinal
Mass Cardinal
7 weeks ago Mark Dunning ★ 1.1k
0
votes
1
reply
362
views
Does anyone have the command to download all of the core_nt using blast_db_get()
rBLAST BiocFileCache
updated 7 weeks ago by 4.1k • written 7 weeks ago by ▴ 380
1
vote
2
replies
1.1k
views
Error in retrieving clinical data
TCGAbiolinks
7 weeks ago • updated 4 weeks ago silickas • 0
1
vote
0
replies
1.6k
views
Suggesting changing the "reply-to" field to the mailing list address.
updated 7 weeks ago by 4.1k • written 15.7 years ago by ▴ 950
0
votes
0
replies
127
views
Help with mouse cell type annotation
annotation SingleR mouse SingleCellData scRNAseq
8 weeks ago Muhammad • 0
0
votes
0
replies
82
views
Unable to restore chromosome sequence lengths or other metadata in BSgenome.Mfascicularis.NCBI.6.0
BSgenome.Mfascicularis.NCBI.6.0
8 weeks ago Genevieve • 0
0
votes
0
replies
78
views
Generating Biphasic Curves in Offline GR Metrics Package
GRmetrics
8 weeks ago Jasmitha • 0
3
votes
5
replies
1.1k
views
Overcoming confounding in batch effect correction
sva BiologicalQuestion
8 weeks ago bbao ▴ 10
0
votes
5
replies
882
views
For some reason I can't update BiocManager to 3.20
Bioconductor
updated 7 weeks ago by 4.1k • written 8 weeks ago by • 0
0
votes
0
replies
89
views
Help with MetagenomeSeq, understanding the 75th quantile
metagenomeSeq cumulativesumscaling
updated 8 weeks ago by 68k • written 9 weeks ago by • 0
0
votes
0
replies
225
views
Methylation data - different probes are classified differently based on transcript? (Illumina methylation arrays, using minfi)
minf minfiDataEPIC MethylationArrayData MethylationArray EPICv2manifest
9 weeks ago charlie.wright • 0
0
votes
4
replies
489
views
Web accessibility of Bioconductor.org
website Website
updated 8 weeks ago by 21k • written 9 weeks ago by • 0
0
votes
0
replies
120
views
Batch Correction while implementing QSEA package
qsea MEDIPS MEDIPSData DNAMethylation
10 weeks ago User3088 • 0
0
votes
1
reply
155
views
building samplesheet and plot profile
DiffBind
10 weeks ago yf • 0
0
votes
0
replies
82
views
DBT JRF & PhD Scholar
BiologicalQuestion OmicsMLRepoR
10 weeks ago Manisha • 0
0
votes
0
replies
126
views
My DEXSeqDataSetFromSE is returning an Error, but all of my checks to seem to indicate that this error is not present
DifferentialSplicing RNASeqData DEXSeq
10 weeks ago cftattersfield • 0
0
votes
2
replies
573
views
How to visualize these pathways using pathview
Salmo_salar RNASeq KEGG pathview
10 weeks ago • updated 8 weeks ago ingrid.h • 0
0
votes
0
replies
98
views
Problem with PCAtool as dependencie
COTAN PCAtools
12 weeks ago Silvia • 0
0
votes
0
replies
116
views
cnvEQTL : Error in cpm.default(y, lib.size = lib.size) : NA counts not allowed
CNVRanger
12 weeks ago xiaofeiwang18266 ▴ 60
0
votes
0
replies
154
views
gsameth GSA: probe annotation to multiple genes
missMethyl gsameth
12 weeks ago nurkenber • 0
1,000 results • Page 1 of 20
Recent ...
Replies
Answer: WGCNA by ATpoint ★ 4.8k
> I would like to ask whether it would make sense to first normalize the count data using DESeq2 and VST before performing WGCNA. This …
Answer: cannot download atena annotation for human by Robert Castelo ★ 3.4k
Hi, sorry for the delay in getting back to you, probably by now you found the solution yourself, but just in case you didn't or anybody els…
Answer: Comparison of results obtained from a subset of the data versus the complete dat by swbarnes2 ★ 1.4k
In general, using the entire dataset and then just comparing the subgroups you want within the whole dataset is preferable.
Comment: Differential expression analysis using two TCGA datasets by ATpoint ★ 4.8k
If these are two different batches then they're fully confounded making it statistically invalid. Biologically, I find it at least question…
Answer: PhD scholar by ATpoint ★ 4.8k
Hi, please consider asking this at biostars.org as here we're mainly answering precise technical questions towards the packages. You are se…
Votes
Answer: Origin of the labels for the SingleCellMultiModal dataset
Answer: PhD scholar
Answer: how to use `arrayWeightsQuick()`?
Answer: how to use `arrayWeightsQuick()`?
Having Trouble Using CNE12() and CNE21() in CNEr
Awards • All
Scholar to ATpoint ★ 4.8k
Popular Question to aguirre ▴ 20
Popular Question to Robert Castelo ★ 3.4k
Scholar to Gordon Smyth 52k
Popular Question to Ariel Chernomoretz ▴ 170
Locations • All
WEHI, Melbourne, Australia, 45 minutes ago
The city by the bay, 1 hour ago
UPF, Barcelona, Spain, 3 hours ago
United States, 3 hours ago
United Kingdom, 3 hours ago
Traffic: 400 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6