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
138
views
Empty table plot using plotGseaTable()
fgsea
17 days ago • updated 15 days ago
Chris
▴ 10
0
votes
0
replies
549
views
what should be the input for SingleR() automatic cell type annotation?
SingleR
11 months ago
Yijing
• 0
0
votes
0
replies
145
views
DEXSeq plot error
DEXSeq
DEXSeqNAvalues
DEXseq
9 weeks ago
jean-christophe.helbling
• 0
0
votes
0
replies
381
views
[Rsamtools] pileup option max_depth behaviour
Rsamtools
pileup
10 months ago
romain.lannes
• 0
0
votes
0
replies
183
views
Could SGSeq utilizes "ts" tag produced from minimap2 other than "XS" tag?
XS-tag
SplicedAlignment
SGSeq
minimap2
11 weeks ago
jk
• 0
2
votes
4
replies
547
views
Different genes expression with limma
DESeq2
DifferentialExpression
limma
updated 4 months ago by
Gordon Smyth
50k • written 5 months ago by
michelafrancesconi8
• 0
0
votes
0
replies
122
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
7 weeks ago
Ankit
▴ 20
0
votes
0
replies
117
views
flowDensity on a flowset
flowDensity
6 weeks ago
fredrikwallberg
• 0
2
votes
6
replies
1.1k
views
Looking for documentation about the use of "split = .sign" in enrichplot's dotplot
enrichplot
3 months ago • updated 12 weeks ago
Tobias
• 0
2
votes
2
replies
2.4k
views
Biostatistician Position: UMass Medical School
Microarray
Microarray
written 16.8 years ago by
David Lapointe
▴ 190
0
votes
2
replies
353
views
combat output NaN
sva
6 months ago
maxixian1990
• 0
0
votes
0
replies
179
views
Comparing the effects of a condition over time in two seperate tissues
MAST
12 weeks ago
Dillon
• 0
1
vote
3
replies
1.9k
views
enrichKEGG results for non-model organism
clusterProfiler
enrichment
KEGG
updated 3 months ago by
cinzia.spagnoli
• 0 • written 23 months ago by
AP
• 0
0
votes
3
replies
285
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 4 weeks ago by
W. Evan Johnson
▴ 850 • written 5 weeks ago by
schlumbohm
• 0
0
votes
0
replies
73
views
Recommendations on deploying cytoviewer shiny.appobj to shinyapps.io?
cytoviewer
ShinyApps
9 days ago
neilzhao
▴ 30
1
vote
3
replies
1.6k
views
regionCounts() from csaw - object 'fancy_mseq' not found
ATACSeq
regionCounts
csaw
updated 5 months ago by
dineika.chandrananda
• 0 • written 2.0 years ago by
zgraytho88
• 0
0
votes
0
replies
154
views
Postdoc
TCGAWorkflow
3 months ago
sameerahmadguru
• 0
0
votes
3
replies
749
views
DECIPHER IdTaxa: Speed up training?
DECIPHER
idtaxa
updated 10 months ago by
Erik Wright
▴ 150 • written 10 months ago by
Till
▴ 30
1
vote
2
replies
687
views
Error running run_app('LFQ')
LFQ
DEPpackage
run_app('LFQ')
ShinyApps
DEP
updated 10 months ago by
Ram
▴ 210 • written 11 months ago by
d.kozhevnikova
▴ 10
0
votes
0
replies
365
views
adding noise to scRNA Seq counts
scRNAseq
10 months ago
Jiyuan
• 0
0
votes
1
reply
288
views
DESeq Design for Time-Series Analysis
RNASeq
DESeq2
timecourse
4 months ago
WS
• 0
0
votes
1
reply
238
views
"Counts" in enrichGO
GSEABase
updated 3 months ago by
Tyler Sagendorf
▴ 10 • written 3 months ago by
Matthew
• 0
1
vote
1
reply
425
views
How do I select a subset of genes for functional enrichment(GO/KEGG) analysis from WGCNA results?
WGCNA
updated 6 months ago by
tangming2005
▴ 190 • written 6 months ago by
meenae
▴ 10
0
votes
0
replies
173
views
rpk per cell saved in SCE object.
SingleCellExperiment
4 months ago
JalapenoCornbread
• 0
2
votes
6
replies
2.0k
views
clusterProfiler for KEGG enrichment (non-model species) Over-Representation Analysis
KEGG
clusterProfiler
updated 4 months ago by
Guido Hooiveld
★ 4.0k • written 14 months ago by
ruiqi.li
▴ 10
0
votes
3
replies
496
views
determine if R package or it's dependencies functionality require internet access
biomaRt
updated 6 months ago by
Gordon Smyth
50k • written 6 months ago by
Marilyn
• 0
0
votes
0
replies
249
views
Can I plot values from LINCS level 4?
cmapR
11 months ago
Alexandre
• 0
1
vote
0
replies
491
views
WGCNA of two different cohorts study
DifferentialExpression
WGCNA
updated 11 months ago by
Michael Love
42k • written 11 months ago by
suphamon.j
▴ 20
0
votes
1
reply
987
views
How to get Cytogenetic band for muscles gene by using Biomart or other tools in R
Annotation
biomaRt
ensembldb
written 2.5 years ago by
Lillian
• 0
2
votes
1
reply
232
views
Only positive enrichment score in GSEA
clusterProfiler
annotation
gseGO
gsea
OrgDb
updated 7 weeks ago by
Guido Hooiveld
★ 4.0k • written 8 weeks ago by
enee
▴ 10
1
vote
0
replies
188
views
Rnaseq sample barcode does not match barcode from TCGA Methylation data
TCGAMethylation450k
MethylationArray
TCGAbiolinks
Tcga
TCGAbiolinksGUI.data
11 weeks ago
BioinfoMug
• 0
0
votes
1
reply
408
views
DESeq2 interaction between one continuous variable and one categorical variable
RNASeqData
DESeq2
updated 6 months ago by
Wolfgang Huber
★ 13k • written 6 months ago by
meroy
• 0
0
votes
0
replies
13
views
Spam:
What happens after 99999 in chrome dinosaur game?
Experimental
4 months ago
larsenlola06
0
0
votes
2
replies
2.7k
views
How to get the rsID of 4 million SNPA
ensembldb
SNP
SNPData
genomes
written 2.2 years ago by
Weiqiong
• 0
0
votes
0
replies
47
views
determine k during RUVSeq
RUVSeq
RUVnormalize
2 days ago
Ειρήνη
• 0
0
votes
0
replies
158
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts
Rsubread
10 weeks ago
chris2.a.white
• 0
0
votes
0
replies
167
views
Can I combine collinear variables into a single value
BatchEffect
limma
11 weeks ago
Harrsha
• 0
0
votes
0
replies
343
views
BubbleGUM for multi group comparison of gene set enrichment
RNASeqData
GeneSetEnrichment
multiGSEA
10 months ago
sonal
• 0
0
votes
0
replies
375
views
Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST
KEGG
RNASeq
6 months ago
mch
• 0
0
votes
0
replies
300
views
Dual species RNA-seq, Library size and normalization
Normalization
edgeR
RNASeq
DESeq2
7 months ago
Florian
• 0
0
votes
0
replies
171
views
To analyze StringTie data using the isoformSwitchAnalyzeR package
IsoformSwitchAnalyzeR
10 weeks ago
Henry
• 0
0
votes
2
replies
264
views
TCGA-GBM subtype tumor
curatedTCGAData
updated 3 months ago by
Marcel Ramos
700 • written 3 months ago by
vicmonm5
• 0
0
votes
3
replies
884
views
How can we use the organism database created by makeorgPackageFromNCBI to KEGG and GO analysis using clusterprofiler package.
clusterProfiler
OrganismDb
updated 5 months ago by
Guido Hooiveld
★ 4.0k • written 5 months ago by
Aastha Kapoor
• 0
0
votes
4
replies
325
views
Interactions in batches of varying size with different number of replicates using limma
limma
RNASeq
DifferentialExpression
11 weeks ago
mperalc
• 0
0
votes
0
replies
384
views
Try to understand better how to set out an effective sample size within the MetagenomSeq package in microbiome ?
Metagenomics
metagenomeSeq
microbiome
phyloseq
microbiomeDataSets
9 months ago
Mohamed
▴ 30
0
votes
0
replies
104
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
5 weeks ago
Stevie Pederson
• 0
0
votes
3
replies
173
views
ChAMP installation issue
Cha
ChAMP
5 days ago • updated 4 days ago
e1271094
• 0
0
votes
1
reply
533
views
Gene enrichment analysis
analysis
R
GOfuncR
updated 11 months ago by
Lluís Revilla Sancho
▴ 730 • written 11 months ago by
Eliza
• 0
0
votes
0
replies
98
views
flowStats for CyTOF
flowStats
16 days ago
tholmes
• 0
0
votes
0
replies
266
views
SomaticSignatures normalization for trinucleotide motifs in reference genome
Normalization
SomaticSignatures
6 months ago
vasily.dobrovolsky
• 0
401 results • Page
2 of 9
Recent ...
Replies
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?
Comment: DESeq2- Mysterious interaction suppresses DEGs
by
shaunpeterson
• 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
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
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
Popular Question
to
Johannes Rainer
★ 2.0k
Locations
• All
EMBL Heidelberg,
2 hours ago
Sweden,
2 hours ago
WEHI, Melbourne, Australia,
2 hours ago
The city by the bay,
3 hours ago
UPF, Barcelona, Spain,
3 hours ago
Traffic: 323 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