1
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4
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522
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DEseq2 coefficient
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11 weeks ago • updated 15 days ago JKim • 0
1
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4
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225
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minfi::read.metharray.exp
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updated 23 days ago by ▴ 780 • written 24 days ago by • 0
1
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4
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353
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
23 days ago • updated 21 days ago winwater0928 • 0
0
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4
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215
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FGSEA pre-ranked input in increasing order or decreasing
fgsea
28 days ago sropri • 0
3
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4
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265
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Store output of matchPWM()
biostrings Biostrings
15 days ago • updated 3 days ago mat149 ▴ 70
0
votes
4
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291
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DEG with low counts
DESeq2
updated 27 days ago by 42k • written 4 weeks ago by • 0
3
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4
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503
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Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
updated 8 days ago by ★ 6.5k • written 11 days ago by • 0
0
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4
replies
262
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Minfi - estimatecellscount
min minfi
updated 17 days ago by 65k • written 6 weeks ago by • 0
0
votes
4
replies
108
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error running enricher from clusterprofiler
clusterProfiler cluster
1 day ago Yael • 0
0
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3
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141
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ChAMP installation issue
Cha ChAMP
4 days ago • updated 3 days ago e1271094 • 0
3
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3
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244
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Reading huge bismark coverage files using bbseq::read.bismark
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4 weeks ago • updated 29 days ago jacques.imbert • 0
0
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3
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173
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Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 27 days ago by 65k • written 27 days ago by ▴ 30
0
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3
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214
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 14 days ago by ★ 4.1k • written 15 days ago by • 0
3
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3
replies
249
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 23 days ago by 42k • written 24 days ago by • 0
2
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3
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261
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package goseq seems to be not available on the latest version of R
goseq
updated 10 days ago by 50k • written 13 days ago by ▴ 20
1
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3
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218
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How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 2 days ago by 50k • written 3 days ago by • 0
0
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3
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219
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Couldn't connect to server while using "pathways"
graphite
updated 10 days ago by 42k • written 11 days ago by • 0
0
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3
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3.7k
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[Mfuzz] Error in cmeans(exprs(eset)
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updated 10 days ago by • 0 • written 13.1 years ago by ▴ 720
1
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3
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886
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How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler RNASeq
updated 23 days ago by ★ 1.2k • written 14 months ago by ▴ 10
3
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3
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366
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permutation test in edgeR
rna-seq edgeR
updated 26 days ago by 50k • written 5 weeks ago by • 0
1
vote
3
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234
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Different Shrunk Log2FC according with reference
DESeq2
updated 22 days ago by 42k • written 23 days ago by ▴ 20
2
votes
3
replies
251
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 12 days ago by ★ 4.1k • written 13 days ago by • 0
0
votes
3
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1.5k
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Limma, eBayes different sample size of groups and adjustment
limma limma
updated 16 days ago by • 0 • written 13.1 years ago by ▴ 10
1
vote
3
replies
250
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 20 days ago by 42k • written 21 days ago by • 0
0
votes
3
replies
184
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Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 16 days ago by ★ 1.9k • written 28 days ago by • 0
0
votes
3
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208
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Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 28 days ago by 50k • written 28 days ago by • 0
5
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3
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304
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Log-cpm values from limma
limma edgeR RNASeq
updated 7 days ago by 50k • written 29 days ago by • 0
2
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3
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1.7k
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ChipQC 'names' attribute [9] must be the same length as the vector [2]'
chipqc
updated 3 days ago by • 0 • written 3.6 years ago by ▴ 60
0
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3
replies
271
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Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 16 days ago by 65k • written 17 days ago by • 0
0
votes
3
replies
299
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 15 days ago by 42k • written 16 days ago by • 0
2
votes
3
replies
78
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Problem installing ChAMP on a MacBook
ChAMP
updated 21 hours ago by 3.9k • written 1 day ago by • 0
3
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3
replies
265
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 18 days ago by ★ 4.1k • written 18 days ago by ▴ 10
0
votes
3
replies
279
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A ComBat-seq issue: the covariates are confounded
ComBat-seq sva
updated 28 days ago by ▴ 850 • written 5 weeks ago by • 0
2
votes
3
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103
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How to correctly adjust for gender in edgeR
design glm edgeR
updated 1 day ago by 50k • written 1 day ago by • 0
0
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3
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89
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Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 1 day ago by 42k • written 2 days ago by • 0
1
vote
3
replies
302
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Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 9 days ago by ★ 4.1k • written 15 days ago by • 0
0
votes
3
replies
8.4k
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SingleR Label.Ont
SingleR
updated 5 days ago by • 0 • written 8 months ago by • 0
1
vote
2
replies
176
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Error in champ.load(): The following specified files do not exist
ChAMP
29 days ago • updated 28 days ago Sherin • 0
1
vote
2
replies
211
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Improving the design matrices vignette in RNAseq123
RNAseq123
25 days ago • updated 10 days ago Lluís Revilla Sancho ▴ 730
1
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2
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107
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Can log2cpm be used for proteomics data normalization?
metaMSdata
2 days ago • updated 1 day ago Daniel • 0
4
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2
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618
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Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
14 days ago • updated 10 days ago gene_bioconductor ▴ 10
0
votes
2
replies
264
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featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_get_next_read_BIN: Assertion `l_name < 256' failed. Aborted (core dumpe…
metaMSdata
24 days ago • updated 22 days ago shuwangxinze1996 • 0
1
vote
2
replies
191
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How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2 eigencorplot PCAtools
3 days ago • updated 14 hours ago BioinfGuru ▴ 30
1
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2
replies
1.0k
views
DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE, : NA/NaN/Inf in foreign function call (arg 1)"
DMRcate Gviz
updated 24 days ago by ▴ 180 • written 14 months ago by ▴ 10
0
votes
2
replies
165
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
17 days ago • updated 14 days ago Aurora • 0
2
votes
2
replies
269
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Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(paste("networks", net.suid, "tables", tbl, sep = "/"), : object 're…
RCy3
5 days ago • updated 16 hours ago Matthew Thornton ▴ 360
0
votes
2
replies
146
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How to make DGEList and design matrix by edgeR package
DGEList edgeR
28 days ago prity6459 • 0
1
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2
replies
75
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Erroe when using makeOrgPackageFromNCBI()
AnnotationForge
2 days ago • updated 1 day ago Patadù ▴ 10
1
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2
replies
173
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Reproducibility issue with scran together with lapply and BiocParallel
scran BiocParallel bluster
22 days ago ATpoint ★ 4.1k
1
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2
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262
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How to retrieve detailed regression results from deseq2
DESeq2
5 weeks ago • updated 27 days ago Weiqian ▴ 10
193 results • Page 2 of 4
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Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db") by Patadù ▴ 10
Hi @marcelramos Thanks for the clarification. Yes, I have installed `org.Vdahlaie.eg.db` using the code you and Guido suggested and now i…
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Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
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Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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