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Votes
0
votes
0
replies
708
views
Catalyst::cluster function does NOT produce the same results when setting seed
visua
Visualization
CATALYST
2.1 years ago
elefth.pavlos
▴ 40
0
votes
1
reply
1.7k
views
WGCNA correlation sign differences between eigen genes/ hub genes and clinical traits
hub
correlation
eigen
WGCNA
updated 2.1 years ago by
Vanatta
• 0 • written 4.1 years ago by
mairah.khan
• 0
2
votes
4
replies
4.5k
views
SingleR annotation of several slots/patients
SingleR
written 2.1 years ago by
Bine
▴ 50
1
vote
1
reply
860
views
How to read fcs3.2 files
flowCore
updated 2.1 years ago by
James W. MacDonald
68k • written 2.1 years ago by
Gabriel
▴ 10
0
votes
2
replies
1.2k
views
GENESIS: Can not use GdsGenotypeReader to read a gds file
GENESIS
GWASTools
GDSfile
updated 2.1 years ago by
Stephanie M. Gogarten
▴ 890 • written 2.1 years ago by
Mindy wang
• 0
0
votes
2
replies
815
views
Java error while running HiCDC overview code
JuicerTools
HiC
HiCDCPlus
Java
Juicer
written 2.1 years ago by
IsMM
• 0
0
votes
2
replies
1.0k
views
NCBI protein conversion to CDNA and NCBI gene (in R)
convert
updated 2.1 years ago by
James W. MacDonald
68k • written 2.1 years ago by
R_Page
• 0
2
votes
2
replies
1.9k
views
How does Deseq2 deal with the row with zero when calculating size factors
DESeq2
written 2.1 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
2.1 years ago
drewhaydensteele
• 0
0
votes
8
replies
2.0k
views
GOslim missing GO term
GO.db
GOslim
2.1 years ago
amanda
• 0
0
votes
3
replies
2.0k
views
Obtaining rsIDs with ENSG and variant ID information
rsid
biomaRt
updated 2.1 years ago by
Robert Castelo
★ 3.4k • written 2.1 years ago by
bd2000
▴ 30
8
votes
7
replies
2.4k
views
Why is DMRcate not available for Bioconductor version 3.18?
DMRcate
written 2.1 years ago by
Daniel E. Weeks
▴ 30
1
vote
2
replies
1.5k
views
EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression
edgeR
updated 2.1 years ago by
Gordon Smyth
53k • written 2.1 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 7 months ago by
Geoff
• 0 • written 2.1 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
2.1 years ago
R_Page
• 0
1
vote
1
reply
975
views
Differential gene expression analysis
RNASeqData
RNAseq123
updated 2.1 years ago by
ATpoint
★ 5.0k • written 2.1 years ago by
kaurprab
• 0
0
votes
3
replies
2.7k
views
How can we use the organism database created by makeorgPackageFromNCBI to KEGG and GO analysis using clusterprofiler package.
clusterProfiler
OrganismDb
updated 2.1 years ago by
Guido Hooiveld
★ 4.1k • written 2.1 years ago by
Aastha Kapoor
• 0
0
votes
1
reply
667
views
analysis of overexpressed proteins in metaproteomes
Proteomics
ProteoMM
ProteomicsWorkflow
Proteome
written 2.1 years ago by
ary.lech
▴ 10
0
votes
0
replies
580
views
Rgraphviz - exported (toFile) dot file loses colour and label information
Rgraphviz
2.1 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 2.0 years ago
Levi
• 0
0
votes
0
replies
727
views
multipollutant models
statistics
Regression
r
limma
2.1 years ago
Jitendra
▴ 10
4
votes
4
replies
5.2k
views
How should I run ssGSEA Hallmark Enrichment Analysis?
ssgsea
GSVA
biotype
proteincoding
msigdb
updated 15 months ago by
tifaGis
• 0 • written 2.1 years ago by
snijesh
▴ 200
1
vote
0
replies
675
views
Attempting to import SBML file using R
SBMLR
sbml
rsbm
rsbml
updated 2.1 years ago by
Michael Love
43k • written 2.1 years ago by
isasg
▴ 10
0
votes
1
reply
833
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
959
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
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
4.5k
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
1.5k
views
convert sequences disambiguated with DECIPHER back to FASTA
DECIPHER
FASTA
disambiguate
written 5.6 years ago by
joannew
• 0
3
votes
8
replies
2.2k
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 22 months ago by
Akshay
• 0 • written 2.1 years ago by
Sarah
▴ 10
0
votes
0
replies
1.0k
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
643
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
791
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
763
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
860
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
875
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
yee
• 0
4
votes
12
replies
2.6k
views
Ensembl down???
biomaRt
2.1 years ago
bas_work
▴ 30
0
votes
2
replies
996
views
Batch correction where one of the batches only has a single sample
DESeq2
2.1 years ago
Tom
▴ 10
0
votes
1
reply
763
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
4.1k
views
Cannot connect to ExperimentHub server
ExperimentHub
updated 20 months ago by
Jiayu
• 0 • written 2.1 years ago by
yanling
• 0
0
votes
9
replies
2.3k
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
850
views
WGCNA less samples
RNA-Seq
WGCNA
Worms
2.1 years ago
davca
• 0
0
votes
0
replies
736
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
642
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
1.6k
views
DESeq2 estimateSizeFactors iterate takes too long
RNASeq
DESeq2
2.1 years ago
Karthik
• 0
46,703 results • Page
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