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Votes
0
votes
0
replies
36
views
Plot PCA with ellipses using ggplot
DESeq2
ggplot
PCA
4 hours ago
robledoj13
• 0
0
votes
3
replies
1.0k
views
How to plot gene names in Gviz plotTracks and get the ideogram track to work (US-based)?
gviz
Saccharomyces_cerevisiae
Gviz
ideogram
updated 16 hours ago by
Maryna
• 0 • written 10 months ago by
Michael
• 0
0
votes
0
replies
95
views
Sigmatrix should not contain missing values error in deconvolution using granule
granulator
16 hours ago
louis.der.hammer
• 0
0
votes
0
replies
75
views
Validity of SingleR with very small bulk RNAseq reference
SingleR
18 hours ago
nhaus
▴ 50
0
votes
0
replies
150
views
DESeq2 Likelihood ratio test + contrast option + Volcano plot
DESeq2
volcanoplot
LRT
2 days ago
Eric
• 0
0
votes
0
replies
108
views
Error in serialization
scDblFinder
BiocParallel
2 days ago
Lluís Revilla Sancho
▴ 730
0
votes
1
reply
190
views
Retrieving Package Metadata from Bioconductor API: Versions and Dependencies
metaMSdata
updated 2 days ago by
shepherl
3.9k • written 2 days ago by
Sadman
• 0
0
votes
0
replies
87
views
Using variantAnnotation to put together genotype and consequence information
variantAnn
VariantAnnotation
4 days ago
ramiro.barrantes
▴ 10
0
votes
1
reply
130
views
save.rnb.set warnings when trying to save rnb.set
RnBeads
RnBeads.hg19
MethylationArray
updated 4 days ago by
James W. MacDonald
66k • written 6 days ago by
hayleyw
• 0
0
votes
0
replies
81
views
ASICS to process NMR spectra
ASICS
8 days ago
KONG ZHI XIAN
• 0
0
votes
0
replies
72
views
MAST package: Most appropriate way to perform lrTest for effect of factor with multiple levels in pairwise manner?
MAST
8 days ago
Kelly
• 0
4
votes
9
replies
436
views
Get_interactions is giving the combined score
STRINGdb
updated 2 days ago by
McKayl
• 0 • written 9 days ago by
nkavabhrath03
▴ 20
0
votes
0
replies
116
views
DESeq2 - Outliers influencing sig DEGs, filter counts per group samples, not by all samples
filtering
DESeq2
outliers
9 days ago
smac_head
• 0
0
votes
2
replies
176
views
featureCounts error: Assertion `numOfBuckets > 0' failed
featureCounts
Subread
Bioconductor
9 days ago
Jessica
• 0
0
votes
0
replies
115
views
How to use GAGE with my own metagenomic KOFams data
kegg.gsets
gageData
gage
KEGG
11 days ago
cereyredondo
• 0
0
votes
1
reply
178
views
output from RAIN doesn't look rhythmic
rain
updated 11 days ago by
ATpoint
★ 4.2k • written 11 days ago by
cereyredondo
• 0
0
votes
0
replies
163
views
Linear Mixed Model for Differential Gene Expression in Single-Cell RNAseq with Batch Effects
lmer
MAST
DifferentialExpression
17 days ago
nhaus
▴ 50
3
votes
4
replies
526
views
Differences in Limma and Dreamlet random effects from confounded dataset
limma
dreamlet
18 days ago • updated 17 days ago
jcollier
• 0
0
votes
0
replies
134
views
ChAMP analysis Error: Meth Matrix and UnMeth Matrix seems not paried correctly AND incomplete final line
MethylationArray
methylationArrayAnalysis
ChAMP
18 days ago
Mathu
• 0
0
votes
0
replies
117
views
RUVg spike-in assumption global expression
RUVSeq
RUVnormalize
18 days ago
Erdi
• 0
0
votes
0
replies
5
views
Spam:
Ground Handling Companies in Maldives
alabaster.schemas
db0
18 days ago
vvipflight01
0
0
votes
0
replies
11
views
Spam:
How do professional SEO services enhance user experience on my website?
metaMSdata
20 days ago
Steven
0
0
votes
0
replies
120
views
How to perform a methylation analyisis from beta values matrix and pd.csv
minfiDataEPIC
21 days ago
yemeijie123
• 0
0
votes
0
replies
111
views
Error in bam loading in getUniqueCleavageEvents() in GUIDEseq package
GUIDEseq
21 days ago
StayM
• 0
0
votes
0
replies
40
views
Spam:
GenOMICC DNA biobank
alabaster.schemas
db0
22 days ago
Jolka
0
0
votes
0
replies
153
views
What does evidence of batch effect in bulk rnaseq look like?
surrogatevariables
DESeq2
BatchEffect
bulkrna-seq
sva-seq
23 days ago • updated 22 days ago
BioinfGuru
▴ 30
0
votes
0
replies
118
views
EPIC v2 annotation and BigWig
EPICv2manifest
IlluminaHumanMethylationEPICv2anno.20a1.hg38
23 days ago
MajaVu
• 0
0
votes
0
replies
180
views
Improving Gene Matching for CIBERSORT Deconvolution with Monaco Reference Matrix in Bulk RNA-Seq
DeconRNASeq
AnnotationDbi
org.Hs.eg.db
23 days ago
chunglee13
• 0
0
votes
4
replies
288
views
Trouble Installing DADA2 (warning: R new user)
dada2
updated 23 days ago by
shepherl
3.9k • written 24 days ago by
schott01
• 0
0
votes
0
replies
111
views
Difference in Predictive component of PLS and OPLS Model
Metabolomics
plotGrouper
Bioconductor
ropls
PLSDAbatch
24 days ago
devarti.mahakalkar
• 0
0
votes
0
replies
132
views
Problem with MethylAid ("Cannot get Manifest object for an 'Unknown' array") and Epicv2
minfi
EPICv2manifest
MethylAid
24 days ago
pcibin
• 0
0
votes
1
reply
144
views
Conumee with EPICv2 Segment function
Conu
conumee
updated 2 days ago by
Simon
• 0 • written 25 days ago by
idatta1
• 0
0
votes
1
reply
165
views
single excel file containing methylation beta values does not get loaded in ChAMP
ChAMP
updated 24 days ago by
Basti
▴ 780 • written 25 days ago by
tahirah.yasmin2014
• 0
1
vote
2
replies
186
views
How to get the DMR?
ENmix
25 days ago • updated 24 days ago
Alex
• 0
0
votes
0
replies
103
views
Remove Control Probes from Affymetrix Human Gene 1.0 ST Array probeset version
AffymetrixDataTestFiles
AffymetrixChip
25 days ago
drexjaramel
• 0
0
votes
3
replies
266
views
How to search Pubmed Central or other fulltext literature base using regex?
metaMSdata
Bioconductor
25 days ago
Abiologist
• 0
0
votes
0
replies
115
views
Understanding Differentially Abundant Neighbourhood Identification
miloR
26 days ago • updated 25 days ago
Dario Strbenac
★ 1.5k
0
votes
1
reply
165
views
Species level information couldn't find with DADA2 bioconductor package
Metagenomics
dada2
MicrobiomeData
updated 15 days ago by
nec14cet0pmat
• 0 • written 28 days ago by
abhisek001
• 0
2
votes
1
reply
227
views
Difference between enrichGO results and Enrichr website results
Pathways
GO.db
clusterProfiler
updated 28 days ago by
Guido Hooiveld
★ 4.0k • written 28 days ago by
adrip
• 0
0
votes
0
replies
150
views
Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution
rnaseqGene
RNAseq
29 days ago
JG13
• 0
0
votes
0
replies
138
views
Blacklist regions on DBA object (diffbind)
DiffBind
chipseq
4 weeks ago
gamma.jian
• 0
0
votes
0
replies
118
views
Structural Variant Format Converted for BRASS Format
StructuralVariantAnnotation
4 weeks ago
Dario Strbenac
★ 1.5k
0
votes
0
replies
127
views
Differential Gene Wrapper for Propotion of Detected
scran
4 weeks ago
Dario Strbenac
★ 1.5k
0
votes
9
replies
434
views
Research Project - Expanding search funtionality on the GEO database
GEOquery
GEO
4 weeks ago • updated 28 days ago
gallantk5
• 0
0
votes
0
replies
137
views
Filtering the genesets for fgseaMultiLevel
msigdb
fgsea
msig
5 weeks ago
Tanvi
• 0
0
votes
0
replies
148
views
ligand-receptor-interactions for bulk RNAseq in R
decoupleR
6 weeks ago
silvaesilva.da
• 0
0
votes
0
replies
181
views
BiomaRt attribute "description" doesn't return NCBI's gene summary anymore
biomaRt
6 weeks ago
Reese
• 0
0
votes
0
replies
127
views
Scoreplot for OPLS
splots
6 weeks ago
devarti.mahakalkar
• 0
0
votes
4
replies
339
views
Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression
scran
scater
SingleCellExperiment
edgeR
6 weeks ago
vohara4
• 0
0
votes
0
replies
119
views
Error in drawHeatmap function
GeneOverlap
heatmaps
6 weeks ago
Johanna
• 0
1,000 results • Page
1 of 20
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Replies
Comment: 'path' must be string
by
James W. MacDonald
66k
Yes. We already knew that from the error message, and I told you that in my previous email. The point wasn't to figure out *where* the err…
Comment: 'path' must be string
by
cpierce2
• 0
I ran the debugger and this is the line that causes the error: ``` if (any(startsWith(pkcData[["RTS_ID"]][1L], "RTS")) & any(startsWith(pr…
Comment: Generating surrogate variables across multiple variables of interest
by
Robert
• 0
Yes, we have several biomarkers, and a proteomic set, so we are characterizing each biomarker by it's proteomic association(s). The use for…
Comment: Error running tximeta
by
Guido Hooiveld
★ 4.0k
FYI (since I just finalized a run with `salmon`). For each sample (`.`) an output folder is created that contains 3 files (`cmd_info.json`…
Comment: Error running tximeta
by
Michael Love
42k
Tximeta uses the full directory. There are files that give the key information about the transcriptome. It's not a good idea to selectively…
Votes
Question: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
Answer: Understanding how to contrast two treatments in DESeq2
Answer: Understanding how to contrast two treatments in DESeq2
Cannot extract TxFeatures for a defined GRanges object
Limma time series spline help
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Lluís Revilla Sancho
▴ 730
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to
maltethodberg
▴ 180
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to
Michael Love
42k
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to
Leonardo Collado Torres
★ 1.1k
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to
Gordon Smyth
51k
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