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0
votes
2
replies
1.7k
views
getSRAdbFile() does not work
SRAdb
GEOmetadb
3.4 years ago
jfertaj
▴ 30
0
votes
1
reply
2.7k
views
Complex Heatmap - correlation matrix - how to have exact same annotation with same colors for rows and columns?
R
heatmaps
ComplexHeatmap
Heatma
updated 3.4 years ago by
Zuguang Gu
▴ 290 • written 3.4 years ago by
תום
• 0
0
votes
0
replies
1.1k
views
Cluster profiler - adj p-value differ from Enrichr
clusterProfiler
enrichR
3.4 years ago
angkoo
▴ 10
4
votes
6
replies
2.6k
views
HTSeq command option for single-end reads
HTSeqGenie
3.5 years ago • updated 3.4 years ago
Maryam.sed1400
• 0
0
votes
1
reply
1.5k
views
How does MAST caculate log fc
MAST
3.5 years ago • updated 8 months ago
Chenghao
▴ 10
0
votes
3
replies
2.3k
views
using of z score in Differentially Expression Analysis
RNASeqR
updated 3.5 years ago by
ATpoint
★ 5.0k • written 3.5 years ago by
fatemehfakhari74
• 0
0
votes
1
reply
1.0k
views
Interpret MetaVolcanoR plot
MetaVolcanoR
updated 3.5 years ago by
Kevin Blighe
★ 4.0k • written 3.5 years ago by
JAcky
• 0
0
votes
2
replies
1.6k
views
Microbiome 16S amplicon analysis in dada2
bioinformatics
DADA2
3.5 years ago
anasjamshed1994
• 0
0
votes
0
replies
591
views
Unable to create VariantExperiment object from VCF
VariantExperiment
3.5 years ago
chase.mateusiak
• 0
0
votes
0
replies
569
views
Analyzing peptide library diversity
#diversity
updated 3.5 years ago by
shepherl
4.3k • written 3.5 years ago by
Sara
• 0
0
votes
0
replies
918
views
Prepare data frame of 3 column-lists or matrix of three-column lists from VCF or BAM files
BAM
Segmentation
CINdex
VCF
Data
3.5 years ago
raven1306
• 0
0
votes
1
reply
1.1k
views
rtracklayer import only subset of ranges
rtracklayer
updated 3.5 years ago by
shepherl
4.3k • written 3.5 years ago by
Jake
▴ 90
0
votes
0
replies
853
views
Filtering single-channel Affymetrix probes
filtering
probe
MicroarrayData
3.5 years ago
Fatemeh
• 0
1
vote
2
replies
1.5k
views
conditional command within GRanges
SummarizedExperiment
updated 3.5 years ago by
Marcel Ramos
700 • written 3.5 years ago by
Marcus
• 0
1
vote
1
reply
4.7k
views
How should I set my eps value in cluster profiler?
clusterProfiler
updated 3.5 years ago by
Guido Hooiveld
★ 4.1k • written 3.5 years ago by
ummscr
• 0
0
votes
0
replies
815
views
Free Gibbson energy RNA doublex
GeneExpression
RNAinteract
3.5 years ago
Tamina
• 0
1
vote
0
replies
902
views
How can I properly decode error when using ASICS?
ASICSdata
ASICS
3.5 years ago
nep63
▴ 10
0
votes
0
replies
946
views
Argument is of length zero in variancePartition/Dream
expression
variancePartition
edgeR
3.5 years ago
Jonathan
• 0
1
vote
1
reply
1.3k
views
GSEA with Wikipathways not entirely reproducible
clusterProfiler
updated 3.5 years ago by
Guido Hooiveld
★ 4.1k • written 3.5 years ago by
Susana
• 0
0
votes
0
replies
872
views
DEXSeq aggregated genes/exons result in NA values
RNASeq
R
DEXSeq
3.5 years ago
osieman52
• 0
0
votes
0
replies
1.0k
views
biomaRt, Ensembl, retrieve "Phenotypes" information
Ensembl
biomaRt
3.5 years ago
Hector
• 0
0
votes
0
replies
1.1k
views
A survey of computational setups for Illumina Infinium DNA methylation EPIC array pipeline
DNAMethylation
wateRmelon
Computation
minfi
3.5 years ago
calen.p.ryan
• 0
1
vote
2
replies
1.5k
views
DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscript out of bounds"
DEXSeq
3.5 years ago
Delta._.43
▴ 20
1
vote
0
replies
919
views
Normalization RNA-seq data maSigPro
maSigPro
3.5 years ago
W.a.m.dekker
▴ 10
1
vote
0
replies
1.2k
views
Statistical test for genomic annotation by ChIPseeker
statistics
PeakAnnotation
ChIPseeker
GuangchuangYu
3.5 years ago
arisarkar88
▴ 40
0
votes
2
replies
1.6k
views
OPLS-DA: confidence interval for accuracy metric
Metabolomics
3.5 years ago
Eddie
• 0
0
votes
1
reply
1.1k
views
Issue installing DEP package
DEP
updated 3.5 years ago by
shepherl
4.3k • written 3.5 years ago by
dheeraj.raya
• 0
0
votes
0
replies
828
views
CustomProDB: specify a snp dataset to be used for the SNP annotation
customProDB
3.5 years ago
04.marshal-decibel
• 0
0
votes
3
replies
2.9k
views
I cannot install "microbiome"
GenomeInfoDbData
microbiome
phyloseq
updated 3.5 years ago by
Marcel Ramos
700 • written 3.5 years ago by
kikiki
• 0
0
votes
1
reply
2.0k
views
error in function useDataset of biomaRt
bioma
biomaRt
updated 3.5 years ago by
Basti
▴ 780 • written 3.5 years ago by
Riley Qiu
• 0
0
votes
3
replies
1.7k
views
ROntoTools: Set returned by keggPathwayGraphs is missing 121 pathways reported by keggPathwayNames
KEGGREST
ROntoTools
KEGG
KEGGgraph
3.5 years ago
abf
▴ 30
1
vote
5
replies
2.0k
views
batch effect
TargetScoreData
batchelor
written 3.5 years ago by
Syed Zaheer
▴ 10
0
votes
2
replies
1.5k
views
Rsubread align --R session aborts
RNA
Alignment
Rsubread
3.5 years ago • updated 3.4 years ago
sreekalasn
• 0
0
votes
0
replies
643
views
Can I loosely say that a gene is expressed by simply look at the gene count from RNA-Seq?
RNASeqData
RNASeq
3.5 years ago
Pang
• 0
0
votes
1
reply
2.0k
views
Error in running: classifySingleR from SingleR package
SingleR
SingleCell
updated 3.5 years ago by
ATpoint
★ 5.0k • written 3.5 years ago by
amit.korngut
• 0
0
votes
2
replies
722
views
MAAPER
MAAPER
updated 3.5 years ago by
ATpoint
★ 5.0k • written 3.5 years ago by
Sasha
• 0
0
votes
1
reply
880
views
APAanalyzer
APAlyzer
3.5 years ago
Sasha
• 0
0
votes
3
replies
1.2k
views
Can I create my own, private ExperimentHub instance?
ExperimentHub
3.5 years ago
sandmann.t
▴ 70
0
votes
0
replies
1.7k
views
Boxplot annotation per cluster and column using ComplexHeatmap
ComplexHeatmap
3.5 years ago
gdeniz
• 0
0
votes
1
reply
1.5k
views
DMRfinder findDMRs.r Error - Argument is of length zero
DSS
DMRcaller
updated 2.7 years ago by
Noelia
• 0 • written 3.5 years ago by
Claire
• 0
0
votes
0
replies
634
views
multiple widths using motifmatchr
motifmatchr
3.5 years ago
ltb47
• 0
0
votes
0
replies
854
views
MM-GS plot doesn't show any negative correlation
wgcna
3.5 years ago
shubhankar.pawar
• 0
0
votes
2
replies
1.5k
views
IsoformSwitchAnalyzeR package on mouse data
rnaseq
IsoformSwitchAnalyzeR
updated 3.5 years ago by
k.vitting.seerup
▴ 120 • written 3.5 years ago by
Ryan
• 0
0
votes
1
reply
915
views
Can I force flowStats::quadrantGate to pick a separation point on the upper side of a signal distribution?
flowStats
quadrantGate
3.5 years ago
Christopher
• 0
0
votes
0
replies
1.4k
views
About normalization of the datasets from Harmonized TCGA data
TCGAbiolinks
Proteomics
GENOMICS
bioinformatics
3.5 years ago
qiz218591
• 0
1
vote
7
replies
3.7k
views
Error with slingshot slingPseudotime and slingCurveWeights after using fitGAM from tradeSeq
tradeSeq
slingshot
3.5 years ago
manduchi
▴ 10
0
votes
1
reply
1.1k
views
Regarding Installation of GEOquery
BiocManager
installation
GEOquery
updated 3.5 years ago by
Basti
▴ 780 • written 3.5 years ago by
surinder.chd90
• 0
0
votes
0
replies
1.1k
views
TCGAbiolinks file.type argument
TCGAbiolinks
3.5 years ago
Elizabeth
• 0
0
votes
0
replies
999
views
Displaying large image stacks (e.g. from multiplexed immunohistochemistry) using shiny and EBImage
shiny
EBImage
3.5 years ago
Wolfgang Huber
★ 13k
0
votes
3
replies
7.9k
views
ridgeplot doesn't work: Error in ans[ypos] <- rep(yes, length.out = len)[ypos] : replacement has length zero
clusterProfiler
updated 3.3 years ago by
mttrantrietminh
• 0 • written 3.5 years ago by
Y.K
• 0
1,000 results • Page
19 of 20
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Comment: Error message that there is no package called Biobase
by
DamionLedner99
• 0
thanks for sharing!!! https://cran.r-project.org/
Comment: msmsTests, inconsistent sign between lFC.Av and LogFC
by
Ben
• 0
Continued here due to posting difficulties: Extract from the results table: ``` Inhibitor Vehicle lFC.Av LogFC ... F1 0.0 27…
Answer: DESeq2 for 16S rRNA Analysis
by
James W. MacDonald
68k
The Wald test is only meant for comparison of two groups at a time, so it depends on what you mean by 'analyze across multiple groups at a …
Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list'
by
varying.mastodon.isyn
• 0
Oh, that error! I remember wrestling with that one for hours when I was first learning Python. Turns out I was trying to use a list itself …
Comment: Confirm that OpenStats will not be archived (pryr dependency)
by
Marina
• 0
Thank you!
Votes
Comment: Are transformed values from rlog /vst log2 normalized counts?
Answer: Are transformed values from rlog /vst log2 normalized counts?
A: DESeq2 normalization vs VST vs rlog
Answer: How to directly decet the outlier samples (libraries) in EdgeR pipeline
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