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Creation
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Views
Votes
0
votes
4
replies
366
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 6 days ago by
Ziliang
• 0 • written 16 days ago by
Ian D.
▴ 70
1
vote
4
replies
526
views
DEseq2 coefficient
DESeq2
coefficient
12 weeks ago • updated 16 days ago
JKim
• 0
0
votes
4
replies
216
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
29 days ago
sropri
• 0
0
votes
4
replies
118
views
error running enricher from clusterprofiler
clusterProfiler
cluster
2 days ago
Yael
• 0
3
votes
4
replies
270
views
Store output of matchPWM()
biostrings
Biostrings
16 days ago • updated 4 days ago
mat149
▴ 70
1
vote
3
replies
303
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 9 days ago by
ATpoint
★ 4.1k • written 16 days ago by
angelathuynh5
• 0
0
votes
3
replies
273
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery
ArrayExpress
limma
DifferentialExpression
updated 17 days ago by
James W. MacDonald
65k • written 18 days ago by
SSSJec
• 0
0
votes
3
replies
100
views
Assymetric MA plot with no overall trend
DESeq2
DifferentialExpression
updated 2 days ago by
Michael Love
42k • written 3 days ago by
Kasper
• 0
5
votes
3
replies
304
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 7 days ago by
Gordon Smyth
50k • written 29 days ago by
Shaimaa Gamal
• 0
2
votes
3
replies
91
views
Problem installing ChAMP on a MacBook
ChAMP
updated 1 day ago by
shepherl
3.9k • written 2 days ago by
Galia
• 0
0
votes
3
replies
300
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 16 days ago by
Michael Love
42k • written 17 days ago by
HAK
• 0
0
votes
3
replies
173
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 28 days ago by
James W. MacDonald
65k • written 28 days ago by
bas_work
▴ 30
1
vote
3
replies
235
views
Different Shrunk Log2FC according with reference
DESeq2
updated 23 days ago by
Michael Love
42k • written 23 days ago by
andrebolerbarros
▴ 20
0
votes
3
replies
2.1k
views
maSigPro genes from clusters
masigpro
clustering
updated 13 hours ago by
anne-laure
• 0 • written 7.9 years ago by
ls299
• 0
0
votes
3
replies
210
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 28 days ago by
Gordon Smyth
50k • written 29 days ago by
prity6459
• 0
2
votes
3
replies
1.7k
views
ChipQC 'names' attribute [9] must be the same length as the vector [2]'
chipqc
updated 4 days ago by
bandconductor
• 0 • written 3.6 years ago by
ZheFrench
▴ 60
2
votes
3
replies
112
views
How to correctly adjust for gender in edgeR
design
glm
edgeR
updated 2 days ago by
Gordon Smyth
50k • written 2 days ago by
Guillermo
• 0
0
votes
3
replies
152
views
ChAMP installation issue
Cha
ChAMP
5 days ago • updated 3 days ago
e1271094
• 0
3
votes
3
replies
250
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 24 days ago by
Michael Love
42k • written 25 days ago by
WardDeb
• 0
2
votes
3
replies
262
views
package goseq seems to be not available on the latest version of R
goseq
updated 11 days ago by
Gordon Smyth
50k • written 14 days ago by
Patrycja
▴ 20
3
votes
3
replies
268
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 18 days ago by
ATpoint
★ 4.1k • written 19 days ago by
bioinf
▴ 10
3
votes
3
replies
368
views
permutation test in edgeR
rna-seq
edgeR
updated 26 days ago by
Gordon Smyth
50k • written 5 weeks ago by
Netanel
• 0
0
votes
3
replies
8.6k
views
SingleR Label.Ont
SingleR
updated 6 days ago by
Denis
• 0 • written 8 months ago by
saeed.khalili
• 0
3
votes
3
replies
244
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
5 weeks ago • updated 29 days ago
jacques.imbert
• 0
0
votes
3
replies
70
views
STRINGdb : error with string_db$plot_network()
STRINGdb
updated 12 hours ago by
damian.szk
▴ 80 • written 15 hours ago by
ninidea
• 0
2
votes
3
replies
254
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 12 days ago by
ATpoint
★ 4.1k • written 14 days ago by
Reza
• 0
0
votes
3
replies
219
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 15 days ago by
ATpoint
★ 4.1k • written 16 days ago by
james.zhang20
• 0
0
votes
3
replies
1.5k
views
Limma, eBayes different sample size of groups and adjustment
limma
limma
updated 17 days ago by
XW
• 0 • written 13.1 years ago by
Babara Mueller
▴ 10
1
vote
3
replies
228
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression
TimeCourse
timeOmics
edgeR
RNAseq
updated 3 days ago by
Gordon Smyth
50k • written 4 days ago by
Ashley
• 0
0
votes
3
replies
220
views
Couldn't connect to server while using "pathways"
graphite
updated 11 days ago by
Michael Love
42k • written 11 days ago by
fduguchunhui
• 0
0
votes
3
replies
279
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 29 days ago by
W. Evan Johnson
▴ 850 • written 5 weeks ago by
schlumbohm
• 0
0
votes
3
replies
3.7k
views
[Mfuzz] Error in cmeans(exprs(eset)
Mfuzz
Mfuzz
updated 11 days ago by
Caio
• 0 • written 13.1 years ago by
boczniak767
▴ 720
1
vote
3
replies
252
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 21 days ago by
Michael Love
42k • written 22 days ago by
JalapenoCornbread
• 0
1
vote
3
replies
890
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 23 days ago by
Guangchuang Yu
★ 1.2k • written 14 months ago by
ruiqi.li
▴ 10
0
votes
3
replies
187
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 17 days ago by
Alejandro Reyes
★ 1.9k • written 29 days ago by
Alessia
• 0
1
vote
2
replies
116
views
Can log2cpm be used for proteomics data normalization?
metaMSdata
3 days ago • updated 2 days ago
Daniel
• 0
0
votes
2
replies
159
views
DESeq2 v1.35.0
DESeq2
updated 15 days ago by
Michael Love
42k • written 15 days ago by
Espresso
• 0
1
vote
2
replies
1.0k
views
DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE, : NA/NaN/Inf in foreign function call (arg 1)"
DMRcate
Gviz
updated 25 days ago by
Tim Peters
▴ 180 • written 14 months ago by
jose.ramirez1
▴ 10
1
vote
2
replies
235
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
29 days ago
Le
• 0
0
votes
2
replies
281
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
6 weeks ago • updated 28 days ago
isaac.vock
• 0
1
vote
2
replies
397
views
limma Intercept vs No-intercept models completely changing DMR results?
limma
DMRcate
MethylationArray
EPICV2
updated 14 days ago by
Gordon Smyth
50k • written 14 days ago by
Kim
• 0
0
votes
2
replies
208
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
16 days ago • updated 15 days ago
kcarey
• 0
1
vote
2
replies
738
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
4 weeks ago • updated 21 days ago
Patadù
▴ 10
1
vote
2
replies
288
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
17 days ago • updated 16 days ago
Yveto
• 0
0
votes
2
replies
1.5k
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2
SpikeIn
Normalization
updated 7 days ago by
maria.soler
• 0 • written 16 months ago by
kalavattam
▴ 10
4
votes
2
replies
619
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
15 days ago • updated 11 days ago
gene_bioconductor
▴ 10
0
votes
2
replies
147
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
28 days ago
prity6459
• 0
2
votes
2
replies
269
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
10 days ago • updated 4 days ago
zzrammal
• 0
0
votes
2
replies
946
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation
wgcna
network
updated 2 days ago by
mariakenneth147
• 0 • written 17 months ago by
pharamac
• 0
0
votes
2
replies
928
views
Problem for loading Bioconductor package in R
Bioconductor
written 4.3 years ago by
araaaju
• 0
191 results • Page
2 of 4
Recent ...
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Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
swbarnes2
★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs
by
shaunpeterson
• 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network()
by
damian.szk
▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Comment: STRINGdb : error with string_db$plot_network()
by
ninidea
• 0
> Does the vignette produce the same error? No. Anyway, I finally solved the problem. I don't know why, but I removed: protocol='http' fr…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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