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0
replies
16
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq
scRNAseq
3 hours ago
Bibi
• 0
0
votes
1
reply
27
views
all variables in design formula must be columns in colData (Deseq2) error
BatchQC
batchinDeseq2.
columnsincolData.
updated 2 hours ago by
ATpoint
★ 4.1k • written 6 hours ago by
Galina
• 0
0
votes
1
reply
56
views
Subsetting RNAseq data | voomaByGroup()
limma
updated 2 hours ago by
Gordon Smyth
50k • written 1 day ago by
Anna
• 0
0
votes
0
replies
29
views
ERROR; return code from pthread_create() is 22
affy
1 day ago • updated 7 hours ago
pickingastar
• 0
0
votes
0
replies
34
views
Minor allele data from grch38 giving NAs from getBM ?
BioMartGOGeneSets
allele_freq
biomaRt
getBM
1 day ago • updated 6 hours ago
Abiologist
• 0
0
votes
2
replies
109
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2
PCAplot
RNA-Seq
DesignModel
updated 1 day ago by
Michael Love
42k • written 1 day ago by
shaunpeterson
• 0
0
votes
3
replies
99
views
STRINGdb : error with string_db$plot_network()
STRINGdb
updated 1 day ago by
damian.szk
▴ 80 • written 2 days ago by
ninidea
• 0
0
votes
2
replies
347
views
Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
updated 1 day ago by
Michael Love
42k • written 2 days ago by
Ken C
• 0
0
votes
2
replies
108
views
DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
DECIPHER
2 days ago
makala
• 0
0
votes
0
replies
49
views
determine k during RUVSeq
RUVSeq
RUVnormalize
3 days ago
Ειρήνη
• 0
0
votes
0
replies
49
views
ReactomeGSA for RNASeq
ReactomeGSA
BatchEffect
RNASeqData
3 days ago
Shaimaa Gamal
• 0
0
votes
0
replies
14
views
Spam:
Unveiling Unmatched Best Custom Patches
SIMAT
3 days ago
oliverelijhan
0
0
votes
0
replies
67
views
ChIPseeker peak_Profile_Heatmap color palette
ChIPseeker
3 days ago
Anton01
• 0
2
votes
3
replies
103
views
Problem installing ChAMP on a MacBook
ChAMP
updated 3 days ago by
shepherl
3.9k • written 3 days ago by
Galia
• 0
0
votes
0
replies
44
views
GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO
KEGG
gage
pathview
3 days ago
danalvoronov
▴ 10
0
votes
0
replies
38
views
query regarding how to apply WGCNA on replicates
replicatesRNAseq
WGCNA
3 days ago
k200987
• 0
2
votes
5
replies
214
views
Error while installing BiocManager::install("org.Vdahliae.eg.db")
org.vdahlaie.eg.db
Bioconductor
4 days ago • updated 2 days ago
Patadù
▴ 10
0
votes
4
replies
129
views
error running enricher from clusterprofiler
clusterProfiler
cluster
4 days ago • updated 3 days ago
Yael
• 0
2
votes
3
replies
122
views
How to correctly adjust for gender in edgeR
design
glm
edgeR
updated 3 days ago by
Gordon Smyth
50k • written 4 days ago by
Guillermo
• 0
0
votes
0
replies
38
views
Difference in Contrast in DiffBind
DiffBind
4 days ago
zzrammal
• 0
4
votes
9
replies
250
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2
timecoursedata
GeneExpression
updated 3 days ago by
ATpoint
★ 4.1k • written 4 days ago by
pangtaihin
• 0
1
vote
2
replies
94
views
Erroe when using makeOrgPackageFromNCBI()
AnnotationForge
4 days ago
Patadù
▴ 10
0
votes
3
replies
112
views
Assymetric MA plot with no overall trend
DESeq2
DifferentialExpression
updated 4 days ago by
Michael Love
42k • written 4 days ago by
Kasper
• 0
1
vote
2
replies
127
views
Can log2cpm be used for proteomics data normalization?
metaMSdata
4 days ago • updated 3 days ago
Daniel
• 0
1
vote
0
replies
59
views
News:
Ensembl 112 has been released.
ensembldb
biomaRt
ensemblrelease
5 days ago
Aleena
▴ 30
0
votes
0
replies
54
views
QSEA- Extraction of Normalized methylation across the samples
qsea
ngsReports
correlation
5 days ago
Researcher
• 0
1
vote
3
replies
246
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression
TimeCourse
timeOmics
edgeR
RNAseq
updated 4 days ago by
Gordon Smyth
50k • written 5 days ago by
Ashley
• 0
1
vote
2
replies
242
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2
eigencorplot
PCAtools
5 days ago • updated 2 days ago
BioinfGuru
▴ 30
0
votes
8
replies
500
views
Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2
pcaExplorer
updated 4 days ago by
BioinfGuru
▴ 30 • written 5 days ago by
Eric Katagirya
• 0
0
votes
1
reply
93
views
normalization across different species for DESeq2 analysis
DESeq2
normalization
Normalization
acrossspecies
updated 4 days ago by
Michael Love
42k • written 5 days ago by
piemmea
• 0
0
votes
2
replies
102
views
Problem finding certain variables when importing a public database GSE73103
GSEABase
GenomicDistributionsData
6 days ago • updated 4 days ago
Yveto
• 0
2
votes
1
reply
71
views
How to design DEXSeq formula for multiple variables
DEXSeq
updated 4 days ago by
Alejandro Reyes
★ 1.9k • written 6 days ago by
Sara
• 0
0
votes
3
replies
178
views
ChAMP installation issue
Cha
ChAMP
6 days ago • updated 5 days ago
e1271094
• 0
0
votes
1
reply
137
views
Gene set enrichment analysis
clusterProfiler
GeneSetEnrichment
updated 6 days ago by
Guido Hooiveld
★ 4.0k • written 6 days ago by
aogunbaw
• 0
0
votes
2
replies
129
views
Batch effect correction: methylome data
sesame
BatchEffect
MethylationArray
updated 4 days ago by
zhouwanding
▴ 10 • written 7 days ago by
Seungmin
• 0
2
votes
2
replies
377
views
Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(paste("networks", net.suid, "tables", tbl, sep = "/"), : object 're…
RCy3
7 days ago • updated 2 days ago
Matthew Thornton
▴ 360
0
votes
1
reply
169
views
Differential gene expression analysis results
DESeq2
DifferentialExpression
updated 9 days ago by
ATpoint
★ 4.1k • written 9 days ago by
sajadahmad41454
• 0
0
votes
0
replies
78
views
Recommendations on deploying cytoviewer shiny.appobj to shinyapps.io?
cytoviewer
ShinyApps
9 days ago
neilzhao
▴ 30
0
votes
1
reply
107
views
normalization using Deseq2
DESeq2
rnaseqGene
Normalization
updated 10 days ago by
ATpoint
★ 4.1k • written 10 days ago by
sajadahmad41454
• 0
1
vote
2
replies
271
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq
duplicateCorrelation
limma
voom
10 days ago • updated 9 days ago
Dylan.Sheerin
• 0
2
votes
7
replies
384
views
deseq2 results
DESeq2
DifferentialExpression
rnaseqGene
DifferentialRegulation
11 days ago • updated 8 days ago
sajadahmad41454
• 0
0
votes
0
replies
73
views
Treeio as.treedata function seq lenght error
treeio
11 days ago
nromerov
• 0
2
votes
2
replies
277
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
11 days ago • updated 6 days ago
zzrammal
• 0
3
votes
10
replies
457
views
Extremely small p-values using Limma for proteomic data
Proteomics
limma
updated 9 days ago by
James W. MacDonald
65k • written 12 days ago by
Abbey
• 0
0
votes
1
reply
113
views
Recovering my account credentials on Bioconductor
Bioconductor
updated 12 days ago by
shepherl
3.9k • written 12 days ago by
cyril.dalmasso
• 0
2
votes
1
reply
173
views
minfi latest update for EPIC V2 chip
minfi
minfiDataEPIC
updated 12 days ago by
James W. MacDonald
65k • written 12 days ago by
e1271094
• 0
0
votes
0
replies
93
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
12 days ago
Dinesh
• 0
3
votes
5
replies
296
views
Help with running egsea()
EGSEA
12 days ago • updated 11 days ago
Chris
▴ 10
3
votes
1
reply
150
views
How to save the DEXSeq results
DEXSeq
updated 13 days ago by
Michael Love
42k • written 13 days ago by
Sara
• 0
2
votes
1
reply
143
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 13 days ago by
Michael Love
42k • written 13 days ago by
mat149
▴ 70
1,737 results • Page
1 of 35
Recent ...
Replies
Answer: all variables in design formula must be columns in colData (Deseq2) error
by
ATpoint
★ 4.1k
Your code is poorly readable. Suggest you select and then highlight with markdown using the `10101` button. Generally, colData(dds) must…
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!
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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