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0
votes
0
replies
19
views
RNASeq time course analysis, missing time points for control
RNASeqData
RnaSeqSampleSize
RNASeq
RNASeqPower
3 hours ago
drewhaydensteele
• 0
0
votes
1
reply
58
views
NCBI protein conversion to CDNA and NCBI gene (in R)
convert
updated 11 hours ago by
Gordon Smyth
48k • written 19 hours ago by
R_Page
• 0
0
votes
1
reply
43
views
Obtaining rsIDs with ENSG and variant ID information
rsid
biomaRt
updated 2 days ago by
Robert Castelo
★ 3.0k • written 2 days ago by
bd2000
• 0
0
votes
8
replies
174
views
GOslim missing GO term
GO.db
GOslim
2 days ago • updated 1 day ago
amanda
• 0
7
votes
5
replies
240
views
Why is DMRcate not available for Bioconductor version 3.18?
DMRcate
updated 16 hours ago by
Tim Peters
▴ 150 • written 2 days ago by
Daniel E. Weeks
▴ 30
1
vote
2
replies
83
views
EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression
edgeR
updated 1 day ago by
Gordon Smyth
48k • written 3 days ago by
Jurgen
• 0
3
votes
2
replies
127
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR
limma
voom
RNASeq
muscat
updated 2 days ago by
Gordon Smyth
48k • written 3 days ago by
annikagable
• 0
0
votes
7
replies
201
views
Deleted:No significant MVPs with a BH adjusted P-value below 0.05
ChAMP
updated 3 days ago by
Basti
▴ 740 • written 3 days ago by
486342583
• 0
0
votes
3
replies
134
views
How can we use the organism database created by makeorgPackageFromNCBI to KEGG and GO analysis using clusterprofiler package.
clusterProfiler
OrganismDb
updated 3 days ago by
Guido Hooiveld
★ 3.8k • written 3 days ago by
Aastha Kapoor
• 0
0
votes
0
replies
37
views
analysis of overexpressed proteins in metaproteomes
Proteomics
ProteoMM
ProteomicsWorkflow
Proteome
3 days ago
ary.lech
▴ 10
2
votes
3
replies
152
views
NCBI protein to NCBI cDNA (Ensembl conversions would be great as well) in R
Rstudio
cDNA
ensembldb
NCBI
3 days ago • updated 19 hours ago
R_Page
• 0
0
votes
0
replies
30
views
Rgraphviz - exported (toFile) dot file loses colour and label information
Rgraphviz
3 days ago
sterlinggunn01
• 0
1
vote
1
reply
81
views
Differential gene expression analysis
RNASeqData
RNAseq123
updated 3 days ago by
ATpoint
★ 3.6k • written 3 days ago by
kaurprab
• 0
0
votes
0
replies
39
views
ATACseqQC shiftGAlignmentsList() problem
ATACseqQC
ATACSeq
3 days ago
jfmay
• 0
0
votes
1
reply
110
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData
WGCNA
consensusnetworks
updated 3 days ago by
James W. MacDonald
64k • written 4 days ago by
Levi
• 0
0
votes
0
replies
52
views
multipollutant models
statistics
Regression
r
limma
4 days ago
Jitendra
▴ 10
1
vote
1
reply
75
views
How should I run ssGSEA Hallmark Enrichment Analysis?
ssgsea
GSVA
biotype
proteincoding
msigdb
updated 4 days ago by
Robert Castelo
★ 3.0k • written 4 days ago by
snijesh
▴ 20
0
votes
0
replies
37
views
Attempting to import SBML file using R
SBMLR
sbml
rsbm
rsbml
4 days ago
isasg
• 0
0
votes
1
reply
63
views
SingleR Book Not Found
SingleR
updated 4 days ago by
Peter Hickey
▴ 650 • written 4 days ago by
jgattiker
• 0
0
votes
2
replies
89
views
bam or VCF files from GSE75010
splots
CopyNumberVariationData
updated 4 days ago by
ATpoint
★ 3.6k • written 4 days ago by
ahonya
• 0
3
votes
2
replies
227
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport
DESeq2
updated 4 days ago by
James W. MacDonald
64k • written 4 days ago by
mckinlee.salazar
• 0
0
votes
5
replies
175
views
locateVariant from VariantAnnotation returns wrong results
VariantAnnotation
locateVariant
updated 4 days ago by
James W. MacDonald
64k • written 5 days ago by
nhaus
• 0
0
votes
3
replies
147
views
DESeq: Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative
RNASeqData
DESeq2
5 days ago
Oenone
• 0
2
votes
5
replies
188
views
Problem loading HDF5Array in R 4.3.2
HDF5Array
updated 4 days ago by
Mike Smith
★ 6.2k • written 5 days ago by
Sarah
▴ 10
0
votes
0
replies
52
views
help with converting MSTRG tags with isoformswictanalyzer
stringtie
IsoformSwitchAnalyzeR
pfamAnalyzeR
gtf
updated 5 days ago by
James W. MacDonald
64k • written 5 days ago by
sumitra.20
• 0
1
vote
1
reply
82
views
Lower FDR cutoff gives more gene counts
DESeq2
updated 5 days ago by
Michael Love
41k • written 5 days ago by
Binjie
• 0
2
votes
9
replies
267
views
Ensembl down???
biomaRt
updated 3 days ago by
James W. MacDonald
64k • written 5 days ago by
bas_work
▴ 20
0
votes
4
replies
160
views
Cannot connect to ExperimentHub server
ExperimentHub
6 days ago
yanling
• 0
0
votes
1
reply
101
views
In the 'About_Annotation_Packages_org.Sc.sgd.db_3.17' columns("org.Sc.sgd.db"), the 'CHRLOC' information is not displayed. However, the 'index.txt' f…
org.Sc.sgd.db
updated 6 days ago by
James W. MacDonald
64k • written 6 days ago by
Chih
• 0
0
votes
9
replies
260
views
It's possible to use clusterProfiler without an annotationDBI package
clusterProfiler
7 days ago • updated 4 days ago
nromerov
• 0
0
votes
3
replies
203
views
Deseq2 - Pairwise results from 6 conditions - error non-conformable arguments
DESeq2
8 days ago • updated 6 days ago
claire
• 0
0
votes
1
reply
154
views
Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes
rnaseq
DESeq2
updated 5 days ago by
Michael Love
41k • written 9 days ago by
pl23
• 0
0
votes
2
replies
153
views
Batch correction where one of the batches only has a single sample
DESeq2
9 days ago • updated 6 days ago
Tom
▴ 10
0
votes
1
reply
124
views
DEseq2 : Complex design with a mixture of male and female mice
statistics
DESeq2
updated 5 days ago by
Michael Love
41k • written 9 days ago by
lionel.spinelli
• 0
0
votes
0
replies
44
views
Cannot read biom file in R
RESOLVE
updated 5 days ago by
shepherl
3.6k • written 9 days ago by
Jashvant Kumar
• 0
0
votes
1
reply
106
views
How to get DMR for Infinium methylation EPIC v2
ChAMP
DMRcate
minfi
updated 6 days ago by
James W. MacDonald
64k • written 9 days ago by
rae.alshammari
• 0
3
votes
8
replies
516
views
DropletUtils read10xcounts adds the 12 Cell Multiplexing Oligo tags as gene names
DropletUtils
droplet
written 10 days ago by
pcantalupo
• 0
1
vote
1
reply
95
views
Minimum datasets needed for meta analysis
RnaSeqSampleSize
updated 10 days ago by
Basti
▴ 740 • written 10 days ago by
Durga
▴ 10
2
votes
3
replies
148
views
DESeq2 estimateSizeFactors iterate takes too long
RNASeq
DESeq2
10 days ago • updated 5 days ago
Karthik
• 0
0
votes
0
replies
60
views
Normalising processed Proteomics data in R
Bioconductor
Proteomics
10 days ago
Joshua
• 0
2
votes
1
reply
101
views
DataFrame Printing User Control
S4Vectors
updated 10 days ago by
Hervé Pagès
16k • written 10 days ago by
Dario Strbenac
★ 1.5k
0
votes
1
reply
80
views
Error in reading my csv file in minfi
minfiDataEPIC
minfi
updated 10 days ago by
Basti
▴ 740 • written 10 days ago by
Ana
• 0
3
votes
2
replies
168
views
biomaRtl returns multiple GO terms when filtering on a single GO term in ensembl database
ensembl
biomaRt
10 days ago • updated 5 days ago
henrydionne
▴ 10
0
votes
2
replies
100
views
Help Subsetting DDS for plotPCA for contrast groups
Rstudio
plotPCA
DESeq2
11 days ago • updated 1 day ago
yee
• 0
0
votes
2
replies
125
views
WGCNA less samples
RNA-Seq
WGCNA
Worms
11 days ago • updated 9 days ago
davca
• 0
1
vote
1
reply
138
views
Limma/DESeq2 for unbalanced nested design (paired samples)
limma
DESeq2
updated 5 days ago by
Michael Love
41k • written 11 days ago by
michael.eigenschink
• 0
3
votes
4
replies
246
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats
r
RNASeqData
limma
voom
11 days ago • updated 9 days ago
pl23
• 0
0
votes
1
reply
127
views
How to use DESeq results with LRT vs. with Wald's test
DESeq2
updated 5 days ago by
Michael Love
41k • written 11 days ago by
luise.bellach
• 0
0
votes
3
replies
161
views
'Subtracting' counts on basis of Negative control media and water samples
limma
edgeR
RNASeq
DESeq2
11 days ago • updated 3 days ago
Karthik
• 0
0
votes
2
replies
100
views
FlowSOM error system.file()
FlowSOM
updated 11 days ago by
SamGG
▴ 320 • written 11 days ago by
agus_rizzo
• 0
45,013 results • Page
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Comment: NCBI protein conversion to CDNA and NCBI gene (in R)
by
Gordon Smyth
48k
Continuation of https://support.bioconductor.org/p/9155428/
Comment: Why is DMRcate not available for Bioconductor version 3.18?
by
Tim Peters
▴ 150
Thanks Daniel, Gordon and Lori for flagging this. DSS is only needed for the vignette so I'll remove that section, plus the dependency, som…
Comment: NCBI protein to NCBI cDNA (Ensembl conversions would be great as well) in R
by
R_Page
• 0
Thank you, this works well. As for CDNA, I figured out what I need to find, and have made a new post regarding it.
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
Hello Michael, I am continuing here and need your expert answer on this again I have performed small rna loci and DNA methylation mappin…
Comment: GOslim missing GO term
by
amanda
• 0
Thank you for the advice and many thanks! It is WGCNA analysis. I will try your method today and see if there are some consistencies.
Votes
Answer: Differential gene expression analysis
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Why is DMRcate not available for Bioconductor version 3.18?
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