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
0
votes
0
replies
127
views
Empty table plot using plotGseaTable()
fgsea
11 days ago • updated 9 days ago
Chris
▴ 10
1
vote
2
replies
338
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
5 weeks ago • updated 9 days ago
Kim
• 0
0
votes
0
replies
103
views
dba.plotProfile() plotting and interpretation
DiffBind
9 days ago
Henry
▴ 10
0
votes
2
replies
149
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
13 days ago • updated 10 days ago
Aurora
• 0
0
votes
0
replies
132
views
One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools
TCGA
18 days ago • updated 10 days ago
glaciya2018
• 0
0
votes
2
replies
186
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
11 days ago • updated 10 days ago
kcarey
• 0
0
votes
1
reply
154
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 10 days ago by
Gordon Smyth
50k • written 10 days ago by
z_bahari
• 0
0
votes
1
reply
137
views
Gene-by-sample covariates in limma
Metabolomics
limma
updated 10 days ago by
Gordon Smyth
50k • written 10 days ago by
c53aba27
• 0
0
votes
0
replies
83
views
flowStats for CyTOF
flowStats
10 days ago
tholmes
• 0
0
votes
2
replies
139
views
DESeq2 v1.35.0
DESeq2
updated 10 days ago by
Michael Love
42k • written 10 days ago by
Espresso
• 0
5
votes
6
replies
2.8k
views
Although I successfully installed the package "simpleaffy'' , I cannot library it. Why?
simpleaffy
updated 10 days ago by
James W. MacDonald
65k • written 2.3 years ago by
yanchangjian2019
• 0
0
votes
0
replies
77
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
11 days ago
yvonneh
• 0
0
votes
0
replies
72
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
11 days ago
Ian D.
▴ 70
0
votes
1
reply
114
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 11 days ago by
4r-rtg
• 0
0
votes
3
replies
193
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 11 days ago by
ATpoint
★ 4.1k • written 11 days ago by
james.zhang20
• 0
0
votes
2
replies
178
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 20 days ago by
taur.vil
• 0
1
vote
2
replies
266
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
12 days ago • updated 11 days ago
Yveto
• 0
0
votes
3
replies
283
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 11 days ago by
Michael Love
42k • written 12 days ago by
HAK
• 0
4
votes
0
replies
118
views
News:
Bioconductor 3.19 is Released!
Release
Bioconductor
Packages
Software
11 days ago
shepherl
3.9k
15
votes
17
replies
1.2k
views
Why p value inconsistent when using different number of pathway score?
limma
23 days ago • updated 11 days ago
Chris
▴ 10
0
votes
3
replies
200
views
Store output of matchPWM()
biostrings
Biostrings
updated 11 days ago by
James W. MacDonald
65k • written 12 days ago by
mat149
▴ 70
1
vote
4
replies
500
views
DEseq2 coefficient
DESeq2
coefficient
11 weeks ago • updated 11 days ago
JKim
• 0
3
votes
4
replies
245
views
Help with error using camera() in limma
CAMERA
limma
13 days ago • updated 12 days ago
Chris
▴ 10
2
votes
2
replies
1.1k
views
limma for gene expression analysis with big and unbalanced sample size
limma
microarray
statistics
updated 12 days ago by
XW
• 0 • written 7.9 years ago by
tati6406
• 0
0
votes
3
replies
1.5k
views
Limma, eBayes different sample size of groups and adjustment
limma
limma
updated 12 days ago by
XW
• 0 • written 13.1 years ago by
Babara Mueller
▴ 10
0
votes
1
reply
252
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots
HMMcopy
CopyNumberVariation
updated 12 days ago by
James W. MacDonald
65k • written 13 days ago by
SSSJec
• 0
0
votes
3
replies
261
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery
ArrayExpress
limma
DifferentialExpression
updated 12 days ago by
James W. MacDonald
65k • written 14 days ago by
SSSJec
• 0
15
votes
23
replies
2.0k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
6 weeks ago • updated 13 days ago
Chris
▴ 10
6
votes
19
replies
2.5k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 13 days ago by
Sey R.
• 0 • written 4.6 years ago by
hsbio
▴ 10
0
votes
3
replies
178
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 13 days ago by
Alejandro Reyes
★ 1.9k • written 25 days ago by
Alessia
• 0
1
vote
1
reply
140
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 13 days ago by
Michael Love
42k • written 13 days ago by
marcusn
• 0
0
votes
1
reply
125
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 13 days ago by
Michael Love
42k • written 13 days ago by
Agung
• 0
0
votes
0
replies
84
views
News:
BioC2024 deadlines approaching
BioC2024
Bioconductor
Community
13 days ago
Maria Doyle
▴ 70
0
votes
1
reply
111
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 13 days ago by
shepherl
3.9k • written 13 days ago by
bounlu
• 0
0
votes
1
reply
125
views
putting my own expression data in deseq2
DESeq2
updated 13 days ago by
ATpoint
★ 4.1k • written 13 days ago by
Dev
• 0
2
votes
2
replies
217
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
13 days ago
Chris
▴ 10
0
votes
0
replies
86
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
14 days ago • updated 13 days ago
Chris
▴ 10
0
votes
4
replies
256
views
Minfi - estimatecellscount
min
minfi
updated 14 days ago by
James W. MacDonald
65k • written 6 weeks ago by
clacarion
• 0
3
votes
3
replies
255
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 14 days ago by
ATpoint
★ 4.1k • written 14 days ago by
bioinf
▴ 10
0
votes
0
replies
94
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
19 days ago • updated 14 days ago
Sara
• 0
1
vote
1
reply
142
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 16 days ago by
Leo Lahti
▴ 40 • written 17 days ago by
Dario Strbenac
★ 1.5k
1
vote
7
replies
342
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
17 days ago • updated 16 days ago
pl23
• 0
0
votes
2
replies
220
views
PCA plot suggestions
DESeq2
PCAtools
updated 17 days ago by
Michael Love
42k • written 18 days ago by
Aaliya
• 0
1
vote
2
replies
726
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
26 days ago • updated 17 days ago
ussarizona
▴ 10
1
vote
3
replies
240
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 17 days ago by
Michael Love
42k • written 17 days ago by
JalapenoCornbread
• 0
0
votes
1
reply
155
views
ATACseq merge peaks
DiffBind
updated 17 days ago by
ATpoint
★ 4.1k • written 18 days ago by
Shloka
• 0
1
vote
4
replies
345
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
19 days ago • updated 17 days ago
winwater0928
• 0
2
votes
9
replies
408
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 17 days ago by
James W. MacDonald
65k • written 18 days ago by
Alexandre
• 0
2
votes
5
replies
250
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 17 days ago by
James W. MacDonald
65k • written 19 days ago by
bandconductor
• 0
1
vote
2
replies
167
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
19 days ago • updated 18 days ago
ATpoint
★ 4.1k
189 results • Page
2 of 4
Recent ...
Replies
Comment: Problem finding certain variables when importing a public database GSE73103
by
Guido Hooiveld
★ 3.9k
FWIW: when I would like to make use of publicly available data, I always use the website to explore which metadata is submitted to GEO (and…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
42k
This is `blockLength=200000`, and providing `seg=seg`? It's alright that it's not identical. In the bootstrapped data, you will now have l…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
Thank you, Michael. I used the script shared by you. The genomic distribution of the original and null loci looks like non-stationary. Plea…
Comment: ChAMP installation issue
by
shepherl
3.9k
Without showing the commands you tried and the full output including error it is impossible to help. Please provide additional information…
Answer: Gene set enrichment analysis
by
Guido Hooiveld
★ 3.9k
No, that is not possible. The idea of gene set enrichment analysis (GSEA) is that it checks which gene sets (pathways, GO categories) are e…
Votes
A: DEXSeq time course design
using variable in design formula
differential expression for Single-cell RNAseq data using edgeR
Why p value inconsistent when using different number of pathway score?
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Awards
• All
Popular Question
to
Gordon Smyth
50k
Popular Question
to
maria.soler
• 0
Popular Question
to
Pietro
▴ 40
Popular Question
to
neilzhao
▴ 30
Popular Question
to
ATpoint
★ 4.1k
Locations
• All
Italy,
1 minute ago
Belgium,
3 minutes ago
France,
9 minutes ago
France,
17 minutes ago
United States,
19 minutes ago
Traffic: 899 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