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4
votes
5
replies
312
views
Method to find pathways different between 2 groups
fgsea
GSVA
CAMERA
11 days ago • updated 2 days ago
Chris
▴ 10
0
votes
3
replies
220
views
Couldn't connect to server while using "pathways"
graphite
updated 10 days ago by
Michael Love
42k • written 11 days ago by
fduguchunhui
• 0
2
votes
1
reply
141
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 11 days ago by
Michael Love
42k • written 11 days ago by
mat149
▴ 70
1
vote
1
reply
184
views
Handling multiple differential expression comparisons
DESeq2
updated 12 days ago by
Michael Love
42k • written 13 days ago by
Zainab
▴ 10
2
votes
2
replies
223
views
fgsea significant result
fgsea
12 days ago • updated 11 days ago
Chris
▴ 10
0
votes
44
replies
3.1k
views
How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges
nullranges
updated 3 days ago by
Michael Love
42k • written 15 months ago by
Poonam
• 0
0
votes
6
replies
285
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 13 days ago by
swbarnes2
★ 1.4k • written 14 days ago by
arfranco
▴ 130
1
vote
2
replies
396
views
limma Intercept vs No-intercept models completely changing DMR results?
limma
DMRcate
MethylationArray
EPICV2
updated 13 days ago by
Gordon Smyth
50k • written 13 days ago by
Kim
• 0
2
votes
3
replies
261
views
package goseq seems to be not available on the latest version of R
goseq
updated 11 days ago by
Gordon Smyth
50k • written 13 days ago by
Patrycja
▴ 20
2
votes
3
replies
252
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 12 days ago by
ATpoint
★ 4.1k • written 13 days ago by
Reza
• 0
0
votes
0
replies
117
views
dba.plotProfile() plotting and interpretation
DiffBind
13 days ago
Henry
▴ 10
0
votes
1
reply
172
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 14 days ago by
Gordon Smyth
50k • written 14 days ago by
z_bahari
• 0
0
votes
1
reply
154
views
Gene-by-sample covariates in limma
Metabolomics
limma
updated 14 days ago by
Gordon Smyth
50k • written 14 days ago by
c53aba27
• 0
4
votes
2
replies
619
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
14 days ago • updated 10 days ago
gene_bioconductor
▴ 10
0
votes
0
replies
95
views
flowStats for CyTOF
flowStats
14 days ago
tholmes
• 0
0
votes
2
replies
159
views
DESeq2 v1.35.0
DESeq2
updated 14 days ago by
Michael Love
42k • written 15 days ago by
Espresso
• 0
0
votes
0
replies
88
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
15 days ago
yvonneh
• 0
0
votes
0
replies
83
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
15 days ago
Ian D.
▴ 70
0
votes
1
reply
129
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 15 days ago by
4r-rtg
• 0
0
votes
4
replies
363
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 5 days ago by
Ziliang
• 0 • written 16 days ago by
Ian D.
▴ 70
0
votes
2
replies
206
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
15 days ago • updated 14 days ago
kcarey
• 0
0
votes
3
replies
216
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 15 days ago by
ATpoint
★ 4.1k • written 15 days ago by
james.zhang20
• 0
1
vote
3
replies
302
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 15 days ago by
angelathuynh5
• 0
4
votes
0
replies
134
views
News:
Bioconductor 3.19 is Released!
Release
Bioconductor
Packages
Software
15 days ago
shepherl
3.9k
0
votes
0
replies
134
views
Empty table plot using plotGseaTable()
fgsea
15 days ago • updated 13 days ago
Chris
▴ 10
0
votes
3
replies
299
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 15 days ago by
Michael Love
42k • written 16 days ago by
HAK
• 0
1
vote
2
replies
285
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
16 days ago • updated 15 days ago
Yveto
• 0
0
votes
1
reply
260
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots
HMMcopy
CopyNumberVariation
updated 16 days ago by
James W. MacDonald
65k • written 17 days ago by
SSSJec
• 0
3
votes
4
replies
259
views
Help with error using camera() in limma
CAMERA
limma
17 days ago • updated 16 days ago
Chris
▴ 10
1
vote
1
reply
153
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 17 days ago by
Michael Love
42k • written 17 days ago by
marcusn
• 0
0
votes
2
replies
165
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
17 days ago • updated 14 days ago
Aurora
• 0
0
votes
1
reply
137
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 17 days ago by
Michael Love
42k • written 17 days ago by
Agung
• 0
0
votes
0
replies
92
views
News:
BioC2024 deadlines approaching
BioC2024
Bioconductor
Community
17 days ago
Maria Doyle
▴ 70
0
votes
1
reply
120
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 17 days ago by
shepherl
3.9k • written 17 days ago by
bounlu
• 0
0
votes
1
reply
134
views
putting my own expression data in deseq2
DESeq2
updated 17 days ago by
ATpoint
★ 4.1k • written 17 days ago by
Dev
• 0
2
votes
2
replies
232
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
17 days ago
Chris
▴ 10
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 16 days ago by
James W. MacDonald
65k • written 18 days ago by
SSSJec
• 0
0
votes
0
replies
94
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
18 days ago • updated 17 days ago
Chris
▴ 10
3
votes
3
replies
265
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 18 days ago by
bioinf
▴ 10
1
vote
1
reply
152
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 20 days ago by
Leo Lahti
▴ 40 • written 21 days ago by
Dario Strbenac
★ 1.5k
0
votes
2
replies
225
views
PCA plot suggestions
DESeq2
PCAtools
updated 21 days ago by
Michael Love
42k • written 22 days ago by
Aaliya
• 0
1
vote
3
replies
250
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 21 days ago by
Michael Love
42k • written 21 days ago by
JalapenoCornbread
• 0
0
votes
1
reply
169
views
ATACseq merge peaks
DiffBind
updated 21 days ago by
ATpoint
★ 4.1k • written 22 days ago by
Shloka
• 0
1
vote
2
replies
211
views
Improving the design matrices vignette in RNAseq123
RNAseq123
25 days ago • updated 11 days ago
Lluís Revilla Sancho
▴ 730
1
vote
7
replies
355
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
21 days ago • updated 20 days ago
pl23
• 0
2
votes
9
replies
425
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 21 days ago by
James W. MacDonald
65k • written 22 days ago by
Alexandre
• 0
0
votes
0
replies
141
views
One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools
TCGA
22 days ago • updated 14 days ago
glaciya2018
• 0
1
vote
2
replies
173
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
23 days ago • updated 22 days ago
ATpoint
★ 4.1k
0
votes
1
reply
165
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 22 days ago by
Michael Love
42k • written 22 days ago by
kcarey
• 0
0
votes
0
replies
99
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
23 days ago • updated 18 days ago
Sara
• 0
45,666 results • Page
2 of 914
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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…
Comment: maSigPro genes from clusters
by
anne-laure
• 0
Hello It is a litlle bit late but I do not get how to extract the genes from each cluster identified by see.genes(sigs$sig.genes$Day4vs…
Comment: STRINGdb : error with string_db$plot_network()
by
damian.szk
▴ 80
Your code seems ok. Does the vignette produce the same error? [link to STRINGdb R script vignette][1] [1]: https://www.bioconductor.or…
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
by
Patadù
▴ 10
Hi @marcelramos Thanks for the clarification. Yes, I have installed `org.Vdahlaie.eg.db` using the code you and Guido suggested and now i…
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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