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0
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13
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
3 hours ago
Dinesh
• 0
3
votes
4
replies
83
views
Help with running egsea()
EGSEA
6 hours ago • updated 4 hours ago
Chris
• 0
1
vote
0
replies
198
views
News:
Nominations for Bioconductor Awards 2024!
Recognition
Awards
Bioconductor
Bioc204
6 weeks ago • updated 7 hours ago
shepherl
3.9k
2
votes
1
reply
41
views
How to save the DEXSeq results
DEXSeq
updated 10 hours ago by
Michael Love
41k • written 11 hours ago by
Sara
• 0
3
votes
3
replies
130
views
Method to find pathways different between 2 groups
fgsea
GSVA
CAMERA
updated 10 hours ago by
Robert Castelo
★ 3.3k • written 1 day ago by
Chris
• 0
0
votes
3
replies
80
views
Couldn't connect to server while using "pathways"
graphite
updated 6 hours ago by
Michael Love
41k • written 18 hours ago by
fduguchunhui
• 0
1
vote
1
reply
55
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 11 hours ago by
Michael Love
41k • written 12 hours ago by
mat149
▴ 70
1
vote
3
replies
83
views
Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
updated 2 hours ago by
Hervé Pagès
16k • written 1 day ago by
robersy
• 0
1
vote
1
reply
99
views
Handling multiple differential expression comparisons
DESeq2
updated 1 day ago by
Michael Love
41k • written 3 days ago by
Zainab
▴ 10
2
votes
2
replies
123
views
fgsea significant result
fgsea
2 days ago • updated 1 day ago
Chris
• 0
0
votes
34
replies
2.6k
views
How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges
nullranges
15 months ago • updated 4 hours ago
Poonam
• 0
0
votes
6
replies
214
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 2 days ago by
swbarnes2
★ 1.3k • written 4 days ago by
arfranco
▴ 130
1
vote
2
replies
332
views
limma Intercept vs No-intercept models completely changing DMR results?
limma
DMRcate
MethylationArray
EPICV2
updated 3 days ago by
Gordon Smyth
50k • written 3 days ago by
Kim
• 0
2
votes
3
replies
156
views
package goseq seems to be not available on the latest version of R
goseq
updated 14 hours ago by
Gordon Smyth
50k • written 3 days ago by
Patrycja
▴ 20
2
votes
3
replies
174
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 1 day ago by
ATpoint
★ 4.1k • written 3 days ago by
Reza
• 0
0
votes
0
replies
53
views
dba.plotProfile() plotting and interpretation
DiffBind
3 days ago
Henry
▴ 10
0
votes
1
reply
109
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 4 days ago by
Gordon Smyth
50k • written 4 days ago by
z_bahari
• 0
0
votes
1
reply
101
views
Gene-by-sample covariates in limma
Metabolomics
limma
updated 4 days ago by
Gordon Smyth
50k • written 4 days ago by
c53aba27
• 0
4
votes
2
replies
531
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
4 days ago • updated 8 hours ago
gene_bioconductor
▴ 10
0
votes
0
replies
50
views
flowStats for CyTOF
flowStats
4 days ago
tholmes
• 0
0
votes
2
replies
107
views
DESeq2 v1.35.0
DESeq2
updated 4 days ago by
Michael Love
41k • written 4 days ago by
Espresso
• 0
0
votes
0
replies
48
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
4 days ago
yvonneh
• 0
0
votes
0
replies
44
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
4 days ago
Ian D.
▴ 70
0
votes
1
reply
68
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 4 days ago by
4r-rtg
• 0
0
votes
2
replies
131
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
5 days ago • updated 4 days ago
Ian D.
▴ 70
0
votes
2
replies
137
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
5 days ago • updated 4 days ago
kcarey
• 0
0
votes
3
replies
136
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 4 days ago by
ATpoint
★ 4.1k • written 5 days ago by
james.zhang20
• 0
0
votes
1
reply
142
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 5 days ago by
ATpoint
★ 4.1k • written 5 days ago by
angelathuynh5
• 0
3
votes
0
replies
73
views
News:
Bioconductor 3.19 is Released!
Release
Bioconductor
Packages
Software
5 days ago
shepherl
3.9k
0
votes
0
replies
90
views
Empty table plot using plotGseaTable()
fgsea
5 days ago • updated 3 days ago
Chris
• 0
0
votes
3
replies
156
views
Store output of matchPWM()
biostrings
Biostrings
updated 5 days ago by
James W. MacDonald
65k • written 5 days ago by
mat149
▴ 70
0
votes
3
replies
252
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 5 days ago by
Michael Love
41k • written 6 days ago by
HAK
• 0
1
vote
2
replies
229
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
6 days ago • updated 5 days ago
Yveto
• 0
8
votes
7
replies
1.7k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 16 hours ago by
Sara
• 0 • written 6.7 years ago by
Sylvain Foisy
▴ 80
0
votes
1
reply
228
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots
HMMcopy
CopyNumberVariation
updated 6 days ago by
James W. MacDonald
65k • written 6 days ago by
SSSJec
• 0
3
votes
4
replies
210
views
Help with error using camera() in limma
CAMERA
limma
6 days ago
Chris
• 0
1
vote
1
reply
109
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 6 days ago by
Michael Love
41k • written 6 days ago by
marcusn
• 0
0
votes
2
replies
123
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
6 days ago • updated 3 days ago
Aurora
• 0
0
votes
1
reply
103
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 6 days ago by
Michael Love
41k • written 7 days ago by
Agung
• 0
0
votes
0
replies
63
views
News:
BioC2024 deadlines approaching
BioC2024
Bioconductor
Community
6 days ago
Maria Doyle
▴ 70
0
votes
1
reply
88
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 6 days ago by
shepherl
3.9k • written 6 days ago by
bounlu
• 0
0
votes
1
reply
110
views
putting my own expression data in deseq2
DESeq2
updated 6 days ago by
ATpoint
★ 4.1k • written 6 days ago by
Dev
• 0
2
votes
2
replies
195
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
7 days ago
Chris
• 0
0
votes
3
replies
242
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery
ArrayExpress
limma
DifferentialExpression
updated 6 days ago by
James W. MacDonald
65k • written 7 days ago by
SSSJec
• 0
0
votes
0
replies
75
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
7 days ago
Chris
• 0
3
votes
3
replies
235
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 7 days ago by
ATpoint
★ 4.1k • written 7 days ago by
bioinf
▴ 10
1
vote
1
reply
130
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 10 days ago by
Leo Lahti
▴ 40 • written 10 days ago by
Dario Strbenac
★ 1.5k
0
votes
2
replies
210
views
PCA plot suggestions
DESeq2
PCAtools
updated 10 days ago by
Michael Love
41k • written 11 days ago by
Aaliya
• 0
1
vote
3
replies
222
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 10 days ago by
Michael Love
41k • written 11 days ago by
JalapenoCornbread
• 0
0
votes
1
reply
138
views
ATACseq merge peaks
DiffBind
updated 10 days ago by
ATpoint
★ 4.1k • written 12 days ago by
Shloka
• 0
45,624 results • Page
1 of 913
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Replies
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
by
Hervé Pagès
16k
Indeed. Calculations involving floating point arithmetic are architecture-dependent, and testing the results should be done with `all.equal…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
I will follow what you suggested. I didn't use max gap anywhere. I was following statistic I and regarding the size of features, my small…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
41k
Oh I see, for the second question, I don't have a great answer. I typically think of one set as the anchor, whose ascertainment is driving …
Comment: Help with running egsea()
by
James W. MacDonald
65k
Oh, right. Ideally you would use NCBI (aka Entrez gene) IDs because they are way more likely to be unique. Gene symbols are broken down int…
Comment: Help with running egsea()
by
Chris
• 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
Votes
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
Answer: Trim/Filter out-of-bounds GRanges
Comment: Help with running egsea()
Answer: How to save the DEXSeq results
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