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1
reply
15
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2
PCAplot
RNA-Seq
DesignModel
55 minutes ago • updated 17 minutes ago
shaunpeterson
• 0
0
votes
3
replies
52
views
STRINGdb : error with string_db$plot_network()
STRINGdb
updated 1 hour ago by
damian.szk
▴ 80 • written 4 hours ago by
ninidea
• 0
0
votes
0
replies
21
views
Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
7 hours ago
Ken C
• 0
0
votes
0
replies
20
views
Minor alleles giving NA from R biomart getBM?
biomaRt
minoralleledata
grch38
getBM
9 hours ago • updated 8 hours ago
Jeremy.Clark
• 0
0
votes
0
replies
38
views
determine k during RUVSeq
RUVSeq
RUVnormalize
1 day ago
Ειρήνη
• 0
0
votes
0
replies
37
views
ReactomeGSA for RNASeq
ReactomeGSA
BatchEffect
RNASeqData
1 day ago
Shaimaa Gamal
• 0
0
votes
0
replies
13
views
Spam:
Unveiling Unmatched Best Custom Patches
SIMAT
1 day ago
oliverelijhan
0
0
votes
0
replies
53
views
ChIPseeker peak_Profile_Heatmap color palette
ChIPseeker
1 day ago
Anton01
• 0
0
votes
0
replies
31
views
GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO
KEGG
gage
pathview
1 day ago
danalvoronov
▴ 10
0
votes
0
replies
29
views
query regarding how to apply WGCNA on replicates
replicatesRNAseq
WGCNA
1 day ago
k200987
• 0
0
votes
0
replies
27
views
Difference in Contrast in DiffBind
DiffBind
2 days ago
zzrammal
• 0
0
votes
1
reply
55
views
Retrieving ceRNA data from the starBase or ENCORI Web API
microRNA
starBase
ceRNA
WebAPI
ENCORI
3 days ago • updated 1 day ago
Bhavya
• 0
0
votes
0
replies
44
views
QSEA- Extraction of Normalized methylation across the samples
qsea
ngsReports
correlation
3 days ago
Researcher
• 0
1
vote
2
replies
216
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2
eigencorplot
PCAtools
3 days ago • updated 22 hours ago
BioinfGuru
▴ 30
0
votes
2
replies
82
views
Problem finding certain variables when importing a public database GSE73103
GSEABase
GenomicDistributionsData
4 days ago • updated 3 days ago
Yveto
• 0
0
votes
3
replies
146
views
ChAMP installation issue
Cha
ChAMP
4 days ago • updated 3 days ago
e1271094
• 0
0
votes
0
replies
66
views
Recommendations on deploying cytoviewer shiny.appobj to shinyapps.io?
cytoviewer
ShinyApps
7 days ago
neilzhao
▴ 30
2
votes
7
replies
357
views
deseq2 results
DESeq2
DifferentialExpression
rnaseqGene
DifferentialRegulation
9 days ago • updated 6 days ago
sajadahmad41454
• 0
0
votes
0
replies
67
views
Treeio as.treedata function seq lenght error
treeio
9 days ago
nromerov
• 0
0
votes
0
replies
84
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
10 days ago
Dinesh
• 0
0
votes
0
replies
117
views
dba.plotProfile() plotting and interpretation
DiffBind
14 days ago
Henry
▴ 10
0
votes
0
replies
95
views
flowStats for CyTOF
flowStats
15 days ago
tholmes
• 0
0
votes
0
replies
88
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
15 days ago
yvonneh
• 0
0
votes
0
replies
83
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
15 days ago
Ian D.
▴ 70
0
votes
3
replies
217
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 15 days ago by
ATpoint
★ 4.1k • written 15 days ago by
james.zhang20
• 0
0
votes
0
replies
134
views
Empty table plot using plotGseaTable()
fgsea
15 days ago • updated 13 days ago
Chris
▴ 10
0
votes
0
replies
94
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
18 days ago
Chris
▴ 10
0
votes
0
replies
141
views
One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools
TCGA
22 days ago • updated 14 days ago
glaciya2018
• 0
0
votes
0
replies
99
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
23 days ago • updated 18 days ago
Sara
• 0
0
votes
0
replies
97
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
23 days ago
Dario Strbenac
★ 1.5k
0
votes
8
replies
380
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 22 days ago by
swbarnes2
★ 1.4k • written 24 days ago by
Aaliya
• 0
0
votes
2
replies
264
views
featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_get_next_read_BIN: Assertion `l_name < 256' failed. Aborted (core dumpe…
metaMSdata
24 days ago • updated 22 days ago
shuwangxinze1996
• 0
2
votes
13
replies
476
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
26 days ago • updated 22 days ago
fernanda.backsouza
▴ 10
0
votes
0
replies
94
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
26 days ago
vaxahey107
• 0
0
votes
0
replies
105
views
I am trying to detect alternative splicing.
ASpli
27 days ago
Sebashish
• 0
0
votes
0
replies
132
views
Warning while loading DEP package
DEP
updated 29 days ago by
shepherl
3.9k • written 29 days ago by
Namrata
• 0
1
vote
2
replies
233
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
29 days ago • updated 28 days ago
Le
• 0
1
vote
2
replies
176
views
Error in champ.load(): The following specified files do not exist
ChAMP
29 days ago
Sherin
• 0
0
votes
1
reply
109
views
Input Question for deseq.r
RSeqAn
updated 29 days ago by
ATpoint
★ 4.1k • written 29 days ago by
Nina
• 0
0
votes
4
replies
263
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
4 weeks ago • updated 27 days ago
lonn
• 0
0
votes
0
replies
91
views
Enzyme Engineering
BioTIP
4 weeks ago
bocchemistry
• 0
0
votes
0
replies
105
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
4 weeks ago
Maliha Tabassum
• 0
0
votes
1
reply
135
views
what is the sampleFiles
chipseq
updated 4 weeks ago by
James W. MacDonald
65k • written 4 weeks ago by
zhulin
• 0
0
votes
0
replies
105
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
4 weeks ago
Virangika
• 0
0
votes
0
replies
82
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
4 weeks ago
Henry
▴ 10
0
votes
1
reply
144
views
Deseq2 Rlog transformation
DESeq2
updated 4 weeks ago by
ATpoint
★ 4.1k • written 4 weeks ago by
Sahar
• 0
2
votes
2
replies
190
views
[DiffBind] Obtaining normalization factors
DiffBind
5 weeks ago • updated 4 weeks ago
Henry
▴ 10
0
votes
3
replies
279
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 29 days ago by
W. Evan Johnson
▴ 850 • written 5 weeks ago by
schlumbohm
• 0
0
votes
0
replies
102
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
5 weeks ago
Stevie Pederson
• 0
3
votes
6
replies
304
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
5 weeks ago
nhaus
▴ 30
1,000 results • Page
1 of 20
Recent ...
Replies
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…
Comment: STRINGdb : error with string_db$plot_network()
by
damian.szk
▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Comment: STRINGdb : error with string_db$plot_network()
by
ninidea
• 0
> Does the vignette produce the same error? No. Anyway, I finally solved the problem. I don't know why, but I removed: protocol='http' fr…
Comment: maSigPro genes from clusters
by
anne-laure
• 0
Hello It is a litlle bit late but I do not get how to extract the genes from each cluster identified by see.genes(sigs$sig.genes$Day4vs…
Comment: STRINGdb : error with string_db$plot_network()
by
damian.szk
▴ 80
Your code seems ok. Does the vignette produce the same error? [link to STRINGdb R script vignette][1] [1]: https://www.bioconductor.or…
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
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