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0
votes
1
answer
231
views
1
answer
plotMA in deseq2
deseq2 written 7 months ago by gv • 40 • updated 7 months ago by Michael Love ♦ 23k
0
votes
1
answer
74
views
1
answer
Problem in installing
deseq2 software error written 8 weeks ago by jivarajivaraj • 10 • updated 8 weeks ago by Martin Morgan ♦♦ 23k
2
votes
2
answers
330
views
2
answers
Tximport of quasi-alignment-based RNAseq quantification (Salmon) for use with edgeR
rnaseq edger salmon tximport written 12 months ago by martin.weihrauch • 10 • updated 12 months ago by Aaron Lun • 23k
1
vote
1
answer
157
views
1
answer
Rsamtools isSupplementary argument not working
rsamtools scanbamparam countbam issupplementary scanbamflag written 7 months ago by galeoni • 0 • updated 7 months ago by Martin Morgan ♦♦ 23k
0
votes
1
answer
318
views
1
answer
Error DESeq2 plotCounts invalid class DESeqDataSet object undefined class for slot rowRanges GenomicRangesORGRangesList
deseq2 plotcounts rowranges written 9 months ago by I.Castanho • 50 • updated 9 months ago by Michael Love ♦ 23k
3
votes
1
answer
94
views
1
answer
quant.sf files and tximport, transcripts not recognized
salmon tximport written 6 weeks ago by Merlin • 10 • updated 6 weeks ago by Michael Love ♦ 23k
1
vote
1
answer
217
views
1
answer
Problems with Organism.dplyr
organism.dplyr written 9 months ago by James W. MacDonald ♦ 50k • updated 9 months ago by Martin Morgan ♦♦ 23k
3
votes
1
answer
156
views
1
answer
Error installing graphite
graphite written 6 months ago by Lluís Revilla Sancho • 470 • updated 6 months ago by gabriele.sales • 100
0
votes
1
answer
158
views
1
answer
DESeq2 design model that considers 3 factors
deseq2 multiple factor design written 8 months ago by sandra • 0 • updated 8 months ago by Michael Love ♦ 23k
0
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1
answer
255
views
1
answer
weights must be finite positive value
edger estimatedispersions written 10 months ago by nonCodingGene • 10 • updated 10 months ago by Aaron Lun • 23k
0
votes
0
answers
96
views
0
answers
I am trying to recreate results from an Alzheimer's paper but I can't figure out my linear regression model
microarray limma edger differential gene expression linear regression written 11 weeks ago by ravelarvargas • 0
9
votes
1
answer
624
views
1
answer
Pre-processing RNA-seq data (normalization and transformation) for GSVA
normalization gsva rna-seq transformation gene set variation analysis written 13 months ago by rached • 40
0
votes
0
answers
137
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0
answers
Query based on PMIDs
geoquery sradb written 5 months ago by Deepak Tanwar • 10
2
votes
1
answer
199
views
1
answer
edgeR. Known cancer genes are not differentially expressed?
edger tcga written 5 months ago by rina • 0 • updated 5 months ago by Aaron Lun • 23k
0
votes
0
answers
59
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0
answers
Possibly bug in newSeqExpressionSet function
edaseq software error written 5 weeks ago by jens • 0
0
votes
2
answers
116
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2
answers
Unable to generate feature vector with custom genome in cleanUpdTSeq
bsgenome cleanupdtseq bsgenomeforge written 10 weeks ago by danielle.bilodeau • 0 • updated 10 weeks ago by Julie Zhu • 4.0k
0
votes
1
answer
200
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1
answer
comparing two GOstats result lists
gostats statistics written 11 months ago by sven.schenk • 10 • updated 11 months ago by James W. MacDonald ♦ 50k
0
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0
answers
85
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0
answers
Clustering large dataset
heatmap seqplots cairo graphics device failed to create cairo backend written 11 weeks ago by Marcelo Laia • 430 • updated 11 weeks ago by shepherl ♦♦ 1.4k
2
votes
2
answers
109
views
2
answers
How to get t-statistic values using edgeR?
edger R gsea fgsea t-statistic written 13 days ago by Biologist • 70 • updated 13 days ago by Gordon Smyth ♦ 37k
0
votes
1
answer
125
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1
answer
Interpretation of logFC and pvalues: LRT vs Wald tests in DESeq2
deseq2 written 4 months ago by RS1 • 0 • updated 4 months ago by Michael Love ♦ 23k
0
votes
1
answer
107
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1
answer
DESeq2 overestimates log2Fold Change
deseq2 written 3 months ago by marcomhefti • 0 • updated 3 months ago by James W. MacDonald ♦ 50k
2
votes
1
answer
229
views
1
answer
Recommendations for combining multiple 10x runs into one SingleCellExperiment
simplesinglecell singlecellexperiment dropletutils written 7 months ago by Peter Hickey • 440 • updated 7 months ago by Aaron Lun • 23k
2
votes
1
answer
136
views
1
answer
vennDiagram in Limma package
limma written 3 months ago by MicheK • 0 • updated 3 months ago by James W. MacDonald ♦ 50k
3
votes
1
answer
296
views
1
answer
converting a fasta file to .2bit format
biostrings rtracklayer written 7 months ago by saripalligautam86 • 10 • updated 7 months ago by Hervé Pagès ♦♦ 13k
0
votes
0
answers
188
views
0
answers
Is S4Vectors not able to install in R-3.5.1?
s4vectors r-3.5.1 written 5 months ago by zhang303 • 0
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