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Votes
0
votes
0
replies
13
views
Plot PCA with ellipses using ggplot
DESeq2
ggplot
PCA
57 minutes ago
robledoj13
• 0
0
votes
0
replies
59
views
News:
Bioconductor Package Download Rate Limitation (HTTP 429)
downloads
http429
http
Bioconductor
8 hours ago
shepherl
3.9k
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 12 hours ago by
Maryna
• 0 • written 10 months ago by
Michael
• 0
0
votes
0
replies
75
views
Sigmatrix should not contain missing values error in deconvolution using granule
granulator
13 hours ago
louis.der.hammer
• 0
0
votes
0
replies
63
views
Validity of SingleR with very small bulk RNAseq reference
SingleR
15 hours ago
nhaus
▴ 50
0
votes
9
replies
323
views
'path' must be string
HELP
path
updated 3 hours ago by
James W. MacDonald
66k • written 1 day ago by
cpierce2
• 0
0
votes
4
replies
641
views
Recount3: PCR duplicates
pcrduplicates
recount3
multimappingreads
updated 1 day ago by
ATpoint
★ 4.2k • written 14 months ago by
seline.natalie
• 0
3
votes
5
replies
249
views
A question occur when using DESeq2 on a complex design
DESeq2
rnaseqGene
RNASeq
1 day ago
MedocRafael
• 0
4
votes
2
replies
707
views
DESeq fitNbinomGLMs Warning Issue: In fitNbinomGLMs(objectNZ[fitidx, , drop = FALSE], alpha_hat = alpha_hat[fitidx], : 4189rows had non-positive e…
DESeq2
RNAseq
8 days ago • updated 1 day ago
mila
▴ 10
0
votes
0
replies
141
views
DESeq2 Likelihood ratio test + contrast option + Volcano plot
DESeq2
volcanoplot
LRT
2 days ago
Eric
• 0
0
votes
0
replies
99
views
Error in serialization
scDblFinder
BiocParallel
2 days ago
Lluís Revilla Sancho
▴ 730
0
votes
1
reply
169
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
3
votes
12
replies
2.2k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP
DMRcate
minfi
updated 1 day ago by
Tim Peters
▴ 190 • written 8 months ago by
rae.alshammari
▴ 10
0
votes
3
replies
212
views
Trouble with creating Series RNA-seq normalized counts matrix
GEO
rnaseqGene
RNA
4 days ago • updated 3 days ago
gallantk5
• 0
0
votes
3
replies
269
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData
DESeq2
RNASeq
DifferentialExpression
updated 3 days ago by
ATpoint
★ 4.2k • written 3 days ago by
Mark
• 0
1
vote
1
reply
701
views
Why does greyListChIP return different grey lists every time I newly run the script?
GreyListChIP
updated 3 days ago by
Matt Eldridge
▴ 10 • written 13 days ago by
Giulia
• 0
0
votes
0
replies
84
views
Using variantAnnotation to put together genotype and consequence information
variantAnn
VariantAnnotation
4 days ago
ramiro.barrantes
▴ 10
0
votes
8
replies
412
views
Error running tximeta
tximeta
updated 9 hours ago by
Guido Hooiveld
★ 4.0k • written 10 days ago by
daria.igudesman
• 0
0
votes
4
replies
370
views
Generating surrogate variables across multiple variables of interest
sva
6 days ago • updated 7 hours ago
Robert
• 0
1
vote
6
replies
315
views
limma and Syntactically Invalid Factor Values
limma
updated 1 day ago by
Gordon Smyth
51k • written 4 days ago by
Dario Strbenac
★ 1.5k
1
vote
1
reply
188
views
DEG Analysis using Limma on DSP GeoMx Data: Handling Multiple ROIs per Core
limma
DSP
GeomxTools
6 days ago • updated 3 days ago
Bioinformagician
• 0
0
votes
8
replies
27k
views
SingleR Label.Ont
SingleR
written 10 months ago by
saeed.khalili
• 0
1
vote
3
replies
299
views
Doubt about model in paired samples (intercept ?)
DESeq2
updated 4 days ago by
Michael Love
42k • written 6 days ago by
picasa1983
• 0
0
votes
10
replies
621
views
Two treatments, one control
DESeq2
stageR
16 days ago • updated 4 days ago
alephreish
• 0
0
votes
1
reply
129
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
3
votes
8
replies
24k
views
Deseq: What does "BaseMean" mean?
deseq2
written 5.9 years ago by
183227851
• 0
0
votes
2
replies
728
views
How to correct for a covariate in DESeq2 that is linear with the condition of interest
DESeq2
7 days ago • updated 4 days ago
Fiona
• 0
2
votes
3
replies
260
views
DeSeq2 Model Problems with species, tissue, and tissue status nesting
DESeq2
R
written 8 days ago by
tbiewerh
• 0
1
vote
2
replies
219
views
Parallel comparison of two DNAString objects with IUPAC ambiguities
Biostrings
written 11 days ago by
maltethodberg
▴ 180
1
vote
1
reply
138
views
Differences between core_enrichment from gsePathway and viewPathway
FunctionalAnalysis
clusterProfiler
viewPathway
gsePathway
updated 7 days ago by
Guido Hooiveld
★ 4.0k • written 7 days ago by
Filipe
• 0
0
votes
1
reply
116
views
methylKit problem
methylKit
updated 7 days ago by
alex.gos90
▴ 10 • written 7 days ago by
Krisztina
• 0
1
vote
3
replies
172
views
Create merged ChIP heatmap across conditions
DiffBind
profileplyr
updated 4 days ago by
Rory Stark
★ 5.2k • written 7 days ago by
jesswhitts
• 0
0
votes
0
replies
73
views
ASICS to process NMR spectra
ASICS
7 days ago
KONG ZHI XIAN
• 0
0
votes
0
replies
70
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
3
votes
3
replies
192
views
Limma comparing gene expression between base line and one treatment
limma
updated 7 days ago by
James W. MacDonald
66k • written 8 days ago by
AL
• 0
0
votes
1
reply
117
views
How to rank DEG for GSEA using DEseq2 result ?
DESeq2
limma
GeneSetEnrichment
updated 8 days ago by
ATpoint
★ 4.2k • written 8 days ago by
picasa1983
• 0
0
votes
1
reply
124
views
Run DEXSeq successfully but got a result that padj==1 in all genes
DEXSeq
updated 8 days ago by
ATpoint
★ 4.2k • written 8 days ago by
2406691063
• 0
4
votes
9
replies
434
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
2
votes
5
replies
262
views
Limma - 0 downreg and upreg values
GeoMx
limma
DifferentialExpression
updated 3 days ago by
James W. MacDonald
66k • written 9 days ago by
sop
• 0
0
votes
2
replies
176
views
featureCounts error: Assertion `numOfBuckets > 0' failed
featureCounts
Subread
Bioconductor
9 days ago
Jessica
• 0
4
votes
12
replies
524
views
DGE with a Continuous Variable
DESeq2
model
updated 11 hours ago by
Michael Love
42k • written 10 days ago by
picasa1983
• 0
0
votes
4
replies
309
views
Error from runShinyMethyl() - is(object, "shinyMethylSet") is not TRUE
shinyMethyl
updated 9 days ago by
James W. MacDonald
66k • written 10 days ago by
Courtney
• 0
1
vote
5
replies
395
views
ComplexHeatmap - alter legend position
ComplexHeatmap
15 days ago • updated 8 days ago
Lucy
▴ 60
3
votes
8
replies
621
views
LIMMA 2x2 Factorial Design with Paired Samples
factorialdesign
limma
pairedsamples
updated 2 days ago by
James W. MacDonald
66k • written 11 days ago by
Michael E
• 0
0
votes
1
reply
160
views
T cell subtype annotation
SingleCellExperiment
updated 11 days ago by
James W. MacDonald
66k • written 11 days ago by
georgii.vdovin
• 0
0
votes
1
reply
191
views
minfi - bumphunter value problem
bumphunter
minfiData
minfi
bumphun
updated 11 days ago by
James W. MacDonald
66k • written 15 days ago by
kumakeren16
• 0
5
votes
7
replies
402
views
findOverlaps(), queryHits and subjectHits()
GenomicFiles
updated 8 days ago by
Hervé Pagès
16k • written 11 days ago by
user_bioinfo
• 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
45,886 results • Page
1 of 918
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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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