Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
3
votes
5
replies
292
views
Help with running egsea()
EGSEA
12 days ago • updated 11 days ago
Chris
▴ 10
3
votes
1
reply
149
views
How to save the DEXSeq results
DEXSeq
updated 12 days ago by
Michael Love
42k • written 12 days ago by
Sara
• 0
4
votes
5
replies
326
views
Method to find pathways different between 2 groups
fgsea
GSVA
CAMERA
13 days ago • updated 3 days ago
Chris
▴ 10
0
votes
3
replies
227
views
Couldn't connect to server while using "pathways"
graphite
updated 12 days ago by
Michael Love
42k • written 12 days ago by
fduguchunhui
• 0
2
votes
1
reply
143
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 12 days ago by
Michael Love
42k • written 12 days ago by
mat149
▴ 70
1
vote
1
reply
189
views
Handling multiple differential expression comparisons
DESeq2
updated 13 days ago by
Michael Love
42k • written 15 days ago by
Zainab
▴ 10
2
votes
2
replies
229
views
fgsea significant result
fgsea
14 days ago • updated 13 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 4 days ago by
Michael Love
42k • written 15 months ago by
Poonam
• 0
0
votes
6
replies
294
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 15 days ago by
swbarnes2
★ 1.4k • written 16 days ago by
arfranco
▴ 130
1
vote
2
replies
405
views
limma Intercept vs No-intercept models completely changing DMR results?
limma
DMRcate
MethylationArray
EPICV2
updated 15 days ago by
Gordon Smyth
50k • written 15 days ago by
Kim
• 0
2
votes
3
replies
271
views
package goseq seems to be not available on the latest version of R
goseq
updated 12 days ago by
Gordon Smyth
50k • written 15 days ago by
Patrycja
▴ 20
2
votes
3
replies
254
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 13 days ago by
ATpoint
★ 4.1k • written 15 days ago by
Reza
• 0
0
votes
0
replies
120
views
dba.plotProfile() plotting and interpretation
DiffBind
15 days ago
Henry
▴ 10
0
votes
1
reply
176
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 16 days ago by
Gordon Smyth
50k • written 16 days ago by
z_bahari
• 0
0
votes
1
reply
157
views
Gene-by-sample covariates in limma
Metabolomics
limma
updated 16 days ago by
Gordon Smyth
50k • written 16 days ago by
c53aba27
• 0
4
votes
2
replies
624
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
16 days ago • updated 12 days ago
gene_bioconductor
▴ 10
0
votes
0
replies
99
views
flowStats for CyTOF
flowStats
16 days ago
tholmes
• 0
0
votes
2
replies
163
views
DESeq2 v1.35.0
DESeq2
updated 16 days ago by
Michael Love
42k • written 16 days ago by
Espresso
• 0
0
votes
0
replies
91
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
16 days ago
yvonneh
• 0
0
votes
0
replies
87
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
16 days ago
Ian D.
▴ 70
0
votes
1
reply
134
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 16 days ago by
4r-rtg
• 0
0
votes
4
replies
373
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 7 days ago by
Ziliang
• 0 • written 17 days ago by
Ian D.
▴ 70
0
votes
2
replies
212
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
17 days ago • updated 16 days ago
kcarey
• 0
0
votes
3
replies
224
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 16 days ago by
ATpoint
★ 4.1k • written 17 days ago by
james.zhang20
• 0
1
vote
3
replies
304
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 10 days ago by
ATpoint
★ 4.1k • written 17 days ago by
angelathuynh5
• 0
4
votes
0
replies
142
views
News:
Bioconductor 3.19 is Released!
Release
Bioconductor
Packages
Software
17 days ago
shepherl
3.9k
0
votes
0
replies
139
views
Empty table plot using plotGseaTable()
fgsea
17 days ago • updated 15 days ago
Chris
▴ 10
0
votes
3
replies
302
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 17 days ago by
Michael Love
42k • written 18 days ago by
HAK
• 0
1
vote
2
replies
292
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
18 days ago • updated 17 days ago
Yveto
• 0
0
votes
1
reply
262
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots
HMMcopy
CopyNumberVariation
updated 18 days ago by
James W. MacDonald
65k • written 19 days ago by
SSSJec
• 0
3
votes
4
replies
262
views
Help with error using camera() in limma
CAMERA
limma
18 days ago
Chris
▴ 10
1
vote
1
reply
157
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 18 days ago by
Michael Love
42k • written 18 days ago by
marcusn
• 0
0
votes
2
replies
169
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
18 days ago • updated 15 days ago
Aurora
• 0
0
votes
1
reply
139
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 18 days ago by
Michael Love
42k • written 19 days ago by
Agung
• 0
0
votes
0
replies
94
views
News:
BioC2024 deadlines approaching
BioC2024
Bioconductor
Community
18 days ago
Maria Doyle
▴ 70
0
votes
1
reply
122
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 18 days ago by
shepherl
3.9k • written 19 days ago by
bounlu
• 0
0
votes
1
reply
137
views
putting my own expression data in deseq2
DESeq2
updated 18 days ago by
ATpoint
★ 4.1k • written 18 days ago by
Dev
• 0
2
votes
2
replies
235
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
19 days ago
Chris
▴ 10
0
votes
3
replies
276
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery
ArrayExpress
limma
DifferentialExpression
updated 18 days ago by
James W. MacDonald
65k • written 19 days ago by
SSSJec
• 0
0
votes
0
replies
95
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
19 days ago
Chris
▴ 10
3
votes
3
replies
269
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 19 days ago by
ATpoint
★ 4.1k • written 20 days ago by
bioinf
▴ 10
1
vote
1
reply
153
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 22 days ago by
Leo Lahti
▴ 40 • written 22 days ago by
Dario Strbenac
★ 1.5k
0
votes
2
replies
227
views
PCA plot suggestions
DESeq2
PCAtools
updated 22 days ago by
Michael Love
42k • written 24 days ago by
Aaliya
• 0
1
vote
3
replies
253
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 22 days ago by
Michael Love
42k • written 23 days ago by
JalapenoCornbread
• 0
0
votes
1
reply
171
views
ATACseq merge peaks
DiffBind
updated 22 days ago by
ATpoint
★ 4.1k • written 24 days ago by
Shloka
• 0
1
vote
2
replies
216
views
Improving the design matrices vignette in RNAseq123
RNAseq123
26 days ago • updated 12 days ago
Lluís Revilla Sancho
▴ 730
1
vote
7
replies
359
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
23 days ago • updated 22 days ago
pl23
• 0
2
votes
9
replies
427
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 23 days ago by
James W. MacDonald
65k • written 23 days ago by
Alexandre
• 0
0
votes
0
replies
143
views
One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools
TCGA
23 days ago • updated 15 days ago
glaciya2018
• 0
1
vote
2
replies
176
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
24 days ago • updated 23 days ago
ATpoint
★ 4.1k
45,668 results • Page
2 of 914
Recent ...
Replies
Answer: Subsetting RNAseq data | voomaByGroup()
by
Gordon Smyth
50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
Answer: Numerical differences in DESeq2 output depending on different design matrix cons
by
Michael Love
42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs
by
Michael Love
42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
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?
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
Awards
• All
Popular Question
to
Dario Strbenac
★ 1.5k
Popular Question
to
Vincent J. Carey, Jr.
6.7k
Popular Question
to
Koen Van den Berge
▴ 180
Popular Question
to
shepherl
3.9k
Popular Question
to
Ken C
• 0
Locations
• All
The city by the bay,
1 minute ago
Hong Kong,
18 minutes ago
India,
51 minutes ago
Singapore,
57 minutes ago
Ireland,
1 hour ago
Traffic: 285 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