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News:
Nominations for Bioconductor Awards 2024!
Recognition
Awards
Bioconductor
Bioc204
6 weeks ago • updated just now
shepherl
3.9k
0
votes
1
reply
30
views
How to save the DEXSeq results
DEXSeq
updated 3 hours ago by
Michael Love
41k • written 3 hours ago by
Sara
• 0
3
votes
3
replies
113
views
Method to find pathways different between 2 groups
fgsea
GSVA
CAMERA
updated 3 hours ago by
Robert Castelo
★ 3.3k • written 17 hours ago by
Chris
• 0
0
votes
3
replies
72
views
Couldn't connect to server while using "pathways"
DESeq2
updated 3 hours ago by
James W. MacDonald
65k • written 11 hours ago by
fduguchunhui
• 0
0
votes
1
reply
46
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 4 hours ago by
Michael Love
41k • written 4 hours ago by
mat149
▴ 70
0
votes
2
replies
62
views
Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
updated 5 hours ago by
Vincent J. Carey, Jr.
6.7k • written 21 hours ago by
robersy
• 0
1
vote
1
reply
96
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
118
views
fgsea significant result
fgsea
1 day ago • updated 23 hours ago
Chris
• 0
0
votes
30
replies
2.5k
views
How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges
nullranges
15 months ago • updated 1 hour ago
Poonam
• 0
0
votes
6
replies
206
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 2 days ago by
swbarnes2
★ 1.3k • written 3 days ago by
arfranco
▴ 130
1
vote
2
replies
331
views
limma Intercept vs No-intercept models completely changing DMR results?
limma
DMRcate
MethylationArray
EPICV2
updated 2 days ago by
Gordon Smyth
50k • written 2 days ago by
Kim
• 0
2
votes
3
replies
150
views
package goseq seems to be not available on the latest version of R
goseq
updated 6 hours ago by
Gordon Smyth
50k • written 2 days ago by
Patrycja
▴ 20
2
votes
3
replies
164
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 1 day ago by
ATpoint
★ 4.1k • written 2 days ago by
Reza
• 0
0
votes
0
replies
51
views
dba.plotProfile() plotting and interpretation
DiffBind
3 days ago
Henry
▴ 10
0
votes
1
reply
107
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 3 days ago by
Gordon Smyth
50k • written 3 days ago by
z_bahari
• 0
0
votes
1
reply
101
views
Gene-by-sample covariates in limma
Metabolomics
limma
updated 3 days ago by
Gordon Smyth
50k • written 3 days ago by
c53aba27
• 0
4
votes
2
replies
504
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
3 days ago • updated 41 minutes ago
gene_bioconductor
▴ 10
0
votes
0
replies
47
views
flowStats for CyTOF
flowStats
4 days ago
tholmes
• 0
0
votes
2
replies
102
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
43
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
63
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 4 days ago by
4r-rtg
• 0
0
votes
2
replies
130
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
135
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
4 days ago • updated 3 days ago
kcarey
• 0
0
votes
3
replies
134
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 4 days ago by
ATpoint
★ 4.1k • written 4 days ago by
james.zhang20
• 0
0
votes
1
reply
138
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 4 days ago by
ATpoint
★ 4.1k • written 4 days ago by
angelathuynh5
• 0
3
votes
0
replies
72
views
News:
Bioconductor 3.19 is Released!
Release
Bioconductor
Packages
Software
4 days ago
shepherl
3.9k
0
votes
0
replies
89
views
Empty table plot using plotGseaTable()
fgsea
4 days ago • updated 2 days ago
Chris
• 0
0
votes
3
replies
156
views
Store output of matchPWM()
biostrings
Biostrings
updated 4 days ago by
James W. MacDonald
65k • written 5 days ago by
mat149
▴ 70
0
votes
3
replies
249
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 4 days ago by
Michael Love
41k • written 5 days ago by
HAK
• 0
0
votes
2
replies
226
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
5 days ago • updated 4 days ago
Yveto
• 0
8
votes
7
replies
1.7k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 9 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
208
views
Help with error using camera() in limma
CAMERA
limma
6 days ago • updated 5 days ago
Chris
• 0
1
vote
1
reply
108
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
122
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 6 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
109
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
6 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
1
vote
2
replies
185
views
Improving the design matrices vignette in RNAseq123
RNAseq123
14 days ago • updated 5 hours ago
Lluís Revilla Sancho
▴ 730
0
votes
0
replies
127
views
One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools
TCGA
11 days ago • updated 3 days ago
glaciya2018
• 0
0
votes
2
replies
166
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 13 days ago by
taur.vil
• 0
14
votes
17
replies
1.2k
views
Why p value inconsistent when using different number of pathway score?
limma
16 days ago • updated 4 days ago
Chris
• 0
0
votes
3
replies
167
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 6 days ago by
Alejandro Reyes
★ 1.9k • written 18 days ago by
Alessia
• 0
1
vote
2
replies
301
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
4 weeks ago • updated 2 days ago
Kim
• 0
15
votes
23
replies
2.0k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
5 weeks ago • updated 6 days ago
Chris
• 0
1
vote
4
replies
481
views
DEseq2 coefficient
DESeq2
coefficient
10 weeks ago • updated 4 days ago
JKim
• 0
55 results • Page
1 of 2
Recent ...
Replies
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
gene_bioconductor
▴ 10
Thanks for your thoughtful and detailed comment, Gordon
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
I looked into the genomic distributions. Please see the screenshot attatched ![ distrubution for female loci, boot1 and boot2][1] how do …
Answer: How to save the DEXSeq results
by
Michael Love
41k
If you look at the output here: https://bioconductor.org/packages/release/bioc/vignettes/DEXSeq/inst/doc/DEXSeq.html#4_Testing_for_differe…
Answer: Method to find pathways different between 2 groups
by
Robert Castelo
★ 3.3k
Hi, regarding how could you combine the result from each tool, one option is using a so-called "ensembl method", for instance, the package …
Answer: Couldn't connect to server while using "pathways"
by
James W. MacDonald
65k
As ATpoint already noted, you should proceed from the assumption that your audience knows nothing about what you are doing, and provide eno…
Votes
Answer: Method to find pathways different between 2 groups
Answer: Method to find pathways different between 2 groups
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: Method to find pathways different between 2 groups
Comment: Trying to use enrichGO
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