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Votes
2
votes
2
replies
1.9k
views
How does Deseq2 deal with the row with zero when calculating size factors
DESeq2
written 2.0 years ago by
jiakang
• 0
1
vote
2
replies
1.2k
views
RNASeq time course analysis, missing time points for control
RNASeqData
RnaSeqSampleSize
RNASeq
RNASeqPower
2.0 years ago
drewhaydensteele
• 0
0
votes
8
replies
1.9k
views
GOslim missing GO term
GO.db
GOslim
2.0 years ago
amanda
• 0
0
votes
3
replies
1.9k
views
Obtaining rsIDs with ENSG and variant ID information
rsid
biomaRt
updated 2.0 years ago by
Robert Castelo
★ 3.4k • written 2.0 years ago by
bd2000
▴ 30
8
votes
7
replies
2.4k
views
Why is DMRcate not available for Bioconductor version 3.18?
DMRcate
written 2.0 years ago by
Daniel E. Weeks
▴ 30
1
vote
2
replies
1.4k
views
EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression
edgeR
updated 2.0 years ago by
Gordon Smyth
53k • written 2.0 years ago by
Jurgen
• 0
12
votes
5
replies
5.2k
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR
limma
voom
RNASeq
muscat
updated 6 months ago by
Geoff
• 0 • written 2.0 years ago by
annikagable
• 0
2
votes
3
replies
1.2k
views
NCBI protein to NCBI cDNA (Ensembl conversions would be great as well) in R
Rstudio
cDNA
ensembldb
NCBI
2.0 years ago
R_Page
• 0
1
vote
1
reply
965
views
Differential gene expression analysis
RNASeqData
RNAseq123
updated 2.0 years ago by
ATpoint
★ 5.0k • written 2.0 years ago by
kaurprab
• 0
0
votes
3
replies
2.6k
views
How can we use the organism database created by makeorgPackageFromNCBI to KEGG and GO analysis using clusterprofiler package.
clusterProfiler
OrganismDb
updated 2.0 years ago by
Guido Hooiveld
★ 4.1k • written 2.0 years ago by
Aastha Kapoor
• 0
0
votes
1
reply
654
views
analysis of overexpressed proteins in metaproteomes
Proteomics
ProteoMM
ProteomicsWorkflow
Proteome
written 2.0 years ago by
ary.lech
▴ 10
0
votes
0
replies
574
views
Rgraphviz - exported (toFile) dot file loses colour and label information
Rgraphviz
2.0 years ago
sterlinggunn01
• 0
1
vote
2
replies
1.9k
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData
WGCNA
consensusnetworks
2.1 years ago • updated 24 months ago
Levi
• 0
0
votes
0
replies
717
views
multipollutant models
statistics
Regression
r
limma
2.1 years ago
Jitendra
▴ 10
4
votes
4
replies
5.0k
views
How should I run ssGSEA Hallmark Enrichment Analysis?
ssgsea
GSVA
biotype
proteincoding
msigdb
updated 14 months ago by
tifaGis
• 0 • written 2.1 years ago by
snijesh
▴ 200
1
vote
0
replies
666
views
Attempting to import SBML file using R
SBMLR
sbml
rsbm
rsbml
updated 2.0 years ago by
Michael Love
43k • written 2.1 years ago by
isasg
▴ 10
0
votes
1
reply
824
views
SingleR Book Not Found
SingleR
updated 2.1 years ago by
Peter Hickey
▴ 760 • written 2.1 years ago by
jgattiker
• 0
3
votes
2
replies
1.3k
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport
DESeq2
updated 2.1 years ago by
James W. MacDonald
68k • written 2.1 years ago by
mckinlee.salazar
• 0
0
votes
3
replies
948
views
bam or VCF files from GSE75010
splots
CopyNumberVariationData
written 2.1 years ago by
ahonya
• 0
0
votes
3
replies
1.3k
views
'Subtracting' counts on basis of Negative control media and water samples
limma
edgeR
RNASeq
DESeq2
2.1 years ago • updated 2.0 years ago
Karthik
• 0
0
votes
5
replies
1.2k
views
locateVariant from VariantAnnotation returns wrong results
VariantAnnotation
locateVariant
updated 2.1 years ago by
James W. MacDonald
68k • written 2.1 years ago by
nhaus
▴ 70
3
votes
6
replies
4.4k
views
Result from GSEA for non-model organism not as expected
clusterProfiler
updated 2.1 years ago by
James W. MacDonald
68k • written 3.2 years ago by
Susanne
▴ 10
0
votes
3
replies
2.7k
views
DESeq: Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative
RNASeqData
DESeq2
2.1 years ago
Oenone
• 0
0
votes
2
replies
1.4k
views
convert sequences disambiguated with DECIPHER back to FASTA
DECIPHER
FASTA
disambiguate
written 5.5 years ago by
joannew
• 0
3
votes
8
replies
2.1k
views
DropletUtils read10xcounts adds the 12 Cell Multiplexing Oligo tags as gene names
DropletUtils
droplet
written 2.1 years ago by
pcantalupo
▴ 10
4
votes
6
replies
2.0k
views
Problem loading HDF5Array in R 4.3.2
HDF5Array
updated 21 months ago by
Akshay
• 0 • written 2.1 years ago by
Sarah
▴ 10
0
votes
0
replies
998
views
help with converting MSTRG tags with isoformswictanalyzer
stringtie
IsoformSwitchAnalyzeR
pfamAnalyzeR
gtf
updated 2.1 years ago by
James W. MacDonald
68k • written 2.1 years ago by
sumitra.20
• 0
1
vote
1
reply
624
views
Lower FDR cutoff gives more gene counts
DESeq2
updated 2.1 years ago by
Michael Love
43k • written 2.1 years ago by
Binjie
• 0
1
vote
1
reply
782
views
Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes
rnaseq
DESeq2
updated 2.1 years ago by
Michael Love
43k • written 2.1 years ago by
pl23
• 0
1
vote
1
reply
750
views
Limma/DESeq2 for unbalanced nested design (paired samples)
limma
DESeq2
updated 2.1 years ago by
Michael Love
43k • written 2.1 years ago by
michael.eigenschink
• 0
0
votes
1
reply
849
views
How to use DESeq results with LRT vs. with Wald's test
DESeq2
updated 2.1 years ago by
Michael Love
43k • written 2.1 years ago by
luise.bellach
• 0
0
votes
1
reply
861
views
DEseq2 : Complex design with a mixture of male and female mice
statistics
DESeq2
updated 2.1 years ago by
Michael Love
43k • written 2.1 years ago by
lionel.spinelli
• 0
0
votes
2
replies
1.3k
views
Help Subsetting DDS for plotPCA for contrast groups
Rstudio
plotPCA
DESeq2
2.1 years ago • updated 2.0 years ago
yee
• 0
4
votes
12
replies
2.5k
views
Ensembl down???
biomaRt
2.1 years ago • updated 2.0 years ago
bas_work
▴ 30
0
votes
2
replies
983
views
Batch correction where one of the batches only has a single sample
DESeq2
2.1 years ago
Tom
▴ 10
0
votes
1
reply
758
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 2.1 years ago by
James W. MacDonald
68k • written 2.1 years ago by
Chih
• 0
1
vote
5
replies
4.0k
views
Cannot connect to ExperimentHub server
ExperimentHub
updated 19 months ago by
Jiayu
• 0 • written 2.1 years ago by
yanling
• 0
0
votes
9
replies
2.2k
views
It's possible to use clusterProfiler without an annotationDBI package
clusterProfiler
2.1 years ago
nromerov
• 0
0
votes
3
replies
1.2k
views
Deseq2 - Pairwise results from 6 conditions - error non-conformable arguments
DESeq2
2.1 years ago
claire
• 0
0
votes
2
replies
827
views
WGCNA less samples
RNA-Seq
WGCNA
Worms
2.1 years ago
davca
• 0
0
votes
0
replies
727
views
Cannot read biom file in R
RESOLVE
updated 2.1 years ago by
shepherl
4.2k • written 2.1 years ago by
Jashvant Kumar
• 0
1
vote
1
reply
634
views
Minimum datasets needed for meta analysis
RnaSeqSampleSize
updated 2.1 years ago by
Basti
▴ 780 • written 2.1 years ago by
Durga
▴ 10
2
votes
3
replies
1.5k
views
DESeq2 estimateSizeFactors iterate takes too long
RNASeq
DESeq2
2.1 years ago
Karthik
• 0
2
votes
1
reply
747
views
DataFrame Printing User Control
S4Vectors
updated 2.1 years ago by
Hervé Pagès
16k • written 2.1 years ago by
Dario Strbenac
★ 1.6k
3
votes
2
replies
1.2k
views
biomaRtl returns multiple GO terms when filtering on a single GO term in ensembl database
ensembl
biomaRt
2.1 years ago
henrydionne
▴ 10
3
votes
4
replies
1.4k
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats
r
RNASeqData
limma
voom
2.1 years ago
pl23
• 0
0
votes
0
replies
638
views
Normalising processed Proteomics data in R
Bioconductor
Proteomics
2.1 years ago
Joshua
• 0
0
votes
1
reply
921
views
Error in reading my csv file in minfi
minfiDataEPIC
minfi
updated 2.1 years ago by
Basti
▴ 780 • written 2.1 years ago by
Ana
• 0
2
votes
5
replies
4.2k
views
STRINGdb R package reference class instantiation with v12.0
STRINGdb
updated 20 months ago by
damian.szk
▴ 110 • written 2.1 years ago by
Abhishek
• 0
0
votes
2
replies
977
views
FlowSOM error system.file()
FlowSOM
updated 2.1 years ago by
SamGG
▴ 360 • written 2.1 years ago by
agus_rizzo
• 0
46,696 results • Page
37 of 934
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Answer: NUPOP usage
by
shepherl
4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker?
by
fnfgame
• 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes
by
Erik Wright
▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Michael Love
43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment
by
Michael Love
43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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