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
Post does not exist.
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
11
views
Looking for Josey Wales Jacket?
MethylSeekR
6 hours ago
Shoqz
• 0
0
votes
0
replies
24
views
Differing results with DESeq2
DESeq2
14 hours ago • updated 13 hours ago
hampsdiv
• 0
0
votes
1
reply
167
views
DESeq2 - human data, weird results, troubleshooting
DESeq2
17 hours ago • updated 16 hours ago
bd2000
▴ 30
1
vote
2
replies
414
views
DESeq: Gene is not flagged as differentially expressed despite count data showing differences
DifferentialExpression
DESeq2
updated 17 hours ago by
James W. MacDonald
68k • written 18 hours ago by
ktz
• 0
0
votes
2
replies
287
views
compute_fasta_digest does not match Salmon index hash
tximeta
10 days ago • updated 1 day ago
Alex
• 0
0
votes
0
replies
23
views
News:
Epigenomics data analysis with R and Bioconductor
chipseq
MNaseSeq
ATACSeq
2 days ago
info
▴ 10
1
vote
2
replies
461
views
Gene IDs conversion between Ensembl and NCBI nomenclature for non-model species
annotation
geneIDs
flatheadmullet
updated 2 days ago by
James W. MacDonald
68k • written 2 days ago by
andremicc
• 0
0
votes
1
reply
402
views
News:
List of Deprecated Packages for Bioc3.20
Release
Devel
Bioconductor
5 months ago • updated 2 days ago
shepherl
4.1k
0
votes
1
reply
92
views
Issue with Soft-Thresholding in WGCNA
WGCNA
updated 2 days ago by
dirty.cougar.risi
• 0 • written 2 days ago by
Μαρία
• 0
0
votes
0
replies
18
views
Spam:
Experience lasting confidence with Vidalista 40 mg
org.Sc.sgd.db
3 days ago
irenejoshi07
0
1
vote
2
replies
1.1k
views
Help with the code for "BiocNeighbors::generic_find_knn() function used by scran::quickCluster()
BiocNeighbors
generic_find_knn
scran
quickCluster
6 days ago • updated 5 days ago
Arctic
• 0
0
votes
1
reply
503
views
DESeq2
org.Mmu.eg.db
DESeq2
TimeCourse
DMSOvsdrug
RNASeqData
updated 6 days ago by
ATpoint
★ 4.8k • written 7 days ago by
Cosmic
• 0
0
votes
1
reply
492
views
Mismatch between Illumina Mouse Methylation BeadChip annotation and genome browsers (UCSC/Ensembl)
methylationArrayAnalysis
MethylationArrayData
updated 7 days ago by
James W. MacDonald
68k • written 7 days ago by
luisa.turco
• 0
1
vote
4
replies
1.3k
views
Package developing and interoperation with Bioconductor
Package
Bioconductor
8 days ago • updated 7 days ago
slizchap
• 0
4
votes
6
replies
1.1k
views
Surprising behavior for DEXseq dispersion estimate plot?
DESeq2
DEXSeq
updated 7 days ago by
ATpoint
★ 4.8k • written 4 weeks ago by
Elijah
• 0
0
votes
4
replies
1.1k
views
Error in H5Dclose(h5dataset) when trying to read in kallisto h5 files
tximport
rhdf5
8 days ago • updated 3 days ago
Sofia
• 0
1
vote
1
reply
725
views
ComBat with repeated measures
ComBat
sva
updated 7 days ago by
ATpoint
★ 4.8k • written 8 days ago by
s20
• 0
0
votes
0
replies
42
views
News:
List of Deprecated Packages for Bioc3.21
devel
Release
release
Devel
8 days ago
shepherl
4.1k
0
votes
0
replies
48
views
News:
Bioconductor 3.21 Release Schedule Important Deadlines Approaching
Software
Release
release
8 days ago
shepherl
4.1k
0
votes
0
replies
52
views
Correlation threshold
MethylationArray
methylationArrayAnalysis
StatisticalMethod
9 days ago
user_bioinfo
• 0
0
votes
0
replies
4
views
Spam:
Does Spirit give free refunds?
ncdfFlow
hcg110.db
MethylSeekR
9 days ago
Haggu
10
0
votes
0
replies
28
views
Spam:
Can I change my BA flight to another date?
org.Sc.sgd.db
MafDb.1Kgenomes.phase1.GRCh38
ncdfFlow
9 days ago
Haggu
10
1
vote
0
replies
22
views
Spam:
What is the cheapest day to fly on American Airlines? {Ask_Expert}
cadd.v1.6.hg38
MafDb.1Kgenomes.phase1.GRCh38
ncdfFlow
9 days ago
Haggu
10
0
votes
0
replies
41
views
Spam:
Can I cancel my British Airways flight and get a refund?
CAGEr
gep2pep
hcg110.db
9 days ago
Haggu
10
0
votes
0
replies
8
views
Spam:
vjkftykdtyk
proDA
hcg110.db
zlibbioc
9 days ago
Haggu
10
0
votes
2
replies
636
views
Improving performance of edgeR and limma while adjusting for multiple confounders
edgeR
limma
updated 9 days ago by
ATpoint
★ 4.8k • written 10 days ago by
robinpaul85
• 0
0
votes
2
replies
389
views
Merging EPICV1 and V2 betas
minfiDataEPIC
minfi
updated 7 days ago by
Garbayo
• 0 • written 10 days ago by
rania.alanany
• 0
0
votes
1
reply
177
views
Error in cnetplot
enrichplot
clusterProfiler
updated 10 days ago by
Guido Hooiveld
★ 4.1k • written 16 days ago by
Ayesha
• 0
0
votes
3
replies
492
views
getBM from biomaRt inconsistencies found with .gtf files across multiple species
.gtf
biomaRt
Ensembl
updated 9 days ago by
Mike Smith
★ 6.6k • written 10 days ago by
Benjamin
▴ 20
2
votes
3
replies
646
views
Explanation for ROAST results
CAMERA
limma
updated 9 days ago by
Gordon Smyth
52k • written 10 days ago by
Jay
• 0
0
votes
0
replies
168
views
How do I set up my DESeq analysis when I know a few vehicle control samples provide background effects we don't want to see in any of the subsequent …
DESeq2
RUVSeq
10 days ago
Simran
• 0
1
vote
1
reply
148
views
Merging annotation with differential expression output
annotation
RNASeqData
updated 10 days ago by
James W. MacDonald
68k • written 10 days ago by
AL
• 0
0
votes
2
replies
363
views
Annotation package for Manduca sexta
annotation
Manducasexta
AnnotationData
11 days ago • updated 9 days ago
GA
▴ 10
0
votes
5
replies
276
views
Bioconductor unable to update 'curl'
curl
HELP
11 days ago
kagodwi2
• 0
0
votes
5
replies
505
views
Ensembl site unresponsive via biomaRt
biomaRt
updated 19 hours ago by
darylruiz6545
• 0 • written 11 days ago by
hebda
• 0
0
votes
1
reply
149
views
best way to grouping GSM belonging to different datasets (with different platforms) and compare differential gene expression
GEOquery
updated 11 days ago by
James W. MacDonald
68k • written 14 days ago by
Alexander
• 0
1
vote
2
replies
1.1k
views
CpGs with genomic positions greater than the chromosome size in EPICv2?
EPICv2
EPICv2manifest
15 days ago • updated 8 days ago
Joshua Llano
• 0
1
vote
4
replies
372
views
DESEQ2 looking at main effects while controlling for a continuous variable
DESeq2
15 days ago • updated 10 days ago
Lennie
• 0
4
votes
5
replies
1.3k
views
Using TPM from tximport of Salmon output for singscore
singscore
17 days ago • updated 14 days ago
Kent
• 0
5
votes
3
replies
773
views
Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with multiple cell types
edgeR
limma
voomLmFit
updated 16 days ago by
Gordon Smyth
52k • written 17 days ago by
Devin
▴ 10
2
votes
10
replies
3.9k
views
Problem at champ.load
ChAMPdata
ChAMP
updated 17 days ago by
Josh
• 0 • written 23 months ago by
angel
• 0
0
votes
1
reply
192
views
GAGE kegg.gsets() self-signed certificate error
gageData
gage
17 days ago • updated 15 days ago
Lucas
• 0
0
votes
2
replies
252
views
myvariant error
myvariant
getVariants
updated 17 days ago by
Christelle
• 0 • written 4 weeks ago by
Christelle
• 0
0
votes
4
replies
473
views
Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
DESeq2
TechnicalReplicates
RNASeq
written 17 days ago by
questionanswer
• 0
0
votes
0
replies
42
views
DiffBind multi-tissue comparison
DiffBind
18 days ago
lryrainche
• 0
1
vote
2
replies
396
views
affy::rma results doesn't match with ncbi website
affy
Preprocessing
Microarray
updated 18 days ago by
James W. MacDonald
68k • written 20 days ago by
akp9132
• 0
0
votes
4
replies
273
views
Problem installing package TxDb.Mmusculus.UCSC.mm10.knownGene
TxDb.Mmusculus.UCSC.mm10.knownGene
18 days ago • updated 17 days ago
Wolfgang RAFFELSBERGER
▴ 140
0
votes
0
replies
116
views
fgsea: ranking genes using log2FC and pvalues derived from spline model
fgsea
GeneSetEnrichment
splines
RNASeq
19 days ago
GT
• 0
1
vote
1
reply
775
views
Use of org.Rn.eg.db with GRCr8 reference genome
DESeq2
org.Rn.eg.db
updated 21 days ago by
James W. MacDonald
68k • written 21 days ago by
Erika
• 0
0
votes
2
replies
618
views
Clarification on GOALL / GO2ALLORFs mapping
org.Sc.sgd.db
22 days ago • updated 16 days ago
DavideSant
• 0
46,435 results • Page
1 of 929
Recent ...
Replies
Comment: DESeq2 - human data, weird results, troubleshooting
by
bd2000
▴ 30
I didn't include all of my code the post would be too long. Here's a link to my GitHub if anyone would like to see the full code: [Full Rst…
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin
by
James W. MacDonald
68k
The simple answer is that the within-group variability is much higher for the first gene as compared to the second. The Wald statistic is j…
Comment: DESeq: Gene is not flagged as differentially expressed despite count data showin
by
ATpoint
★ 4.8k
> since there doesn't seem to be as much count variability, No? Your CD45 samples range on normalized scale from 2 to 3255. That's 3 orde…
Comment: Ensembl site unresponsive via biomaRt
by
darylruiz6545
• 0
Thank you so much for sharing the link.
Comment: compute_fasta_digest does not match Salmon index hash
by
Alex
• 0
I use the `fastaDigest` tool from [COMBINE-lab/fastaDigest](https://github.com/COMBINE-lab/FastaDigest/), which has the function `compute_f…
Votes
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin
Two EPIC Methylation Array Analysis Questions
How to get DMR for Infinium methylation EPIC v2
A: GEOquery Fails to Download Series Matrix File
Comment: Gene IDs conversion between Ensembl and NCBI nomenclature for non-model species
Awards
• All
Popular Question
to
bd2000
▴ 30
Popular Question
to
shepherl
4.1k
Scholar
to
Michael Love
43k
Popular Question
to
Rob
• 0
Popular Question
to
Gordon Smyth
52k
Locations
• All
United States,
12 minutes ago
United States,
26 minutes ago
India,
51 minutes ago
The city by the bay,
56 minutes ago
United States,
2 hours ago
Traffic: 473 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