2
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4
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1.7k
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EGSEA usage with microarray data (with vooma)?
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updated 8 days ago by ▴ 10 • written 7.4 years ago by ▴ 190
0
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4
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360
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More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 5 days ago by • 0 • written 16 days ago by ▴ 70
0
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4
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262
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
29 days ago • updated 27 days ago lonn • 0
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4
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News: European Bioconductor Conference 2023 planning
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updated 4 hours ago by • 0 • written 19 months ago by ▴ 70
0
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4
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262
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Minfi - estimatecellscount
min minfi
updated 17 days ago by 65k • written 6 weeks ago by • 0
0
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4
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291
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DEG with low counts
DESeq2
updated 28 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 9 days ago by ★ 6.5k • written 11 days ago by • 0
1
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4
replies
354
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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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3
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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
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3
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252
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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
1
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3
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234
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Different Shrunk Log2FC according with reference
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updated 22 days ago by 42k • written 23 days ago by ▴ 20
3
votes
3
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244
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Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array BiocGenerics BiocParallel Biobase
5 weeks ago • updated 29 days ago jacques.imbert • 0
0
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3
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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
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 2 days ago by 42k • written 2 days ago by • 0
1
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3
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888
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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
1
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3
replies
302
views
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
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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
0
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3
replies
214
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 15 days ago by ★ 4.1k • written 15 days ago by • 0
0
votes
3
replies
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
2
votes
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
1
vote
3
replies
250
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 20 days ago by 42k • written 21 days ago by • 0
5
votes
3
replies
304
views
Log-cpm values from limma
limma edgeR RNASeq
updated 7 days ago by 50k • written 29 days ago by • 0
1
vote
3
replies
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
3
votes
3
replies
265
views
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
220
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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
3
votes
3
replies
366
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permutation test in edgeR
rna-seq edgeR
updated 26 days ago by 50k • written 5 weeks ago by • 0
3
votes
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
0
votes
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
2
votes
3
replies
104
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How to correctly adjust for gender in edgeR
design glm edgeR
updated 1 day ago by 50k • written 2 days ago by • 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
0
votes
3
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3.7k
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[Mfuzz] Error in cmeans(exprs(eset)
Mfuzz Mfuzz
updated 10 days ago by • 0 • written 13.1 years ago by ▴ 720
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 29 days ago by • 0
2
votes
3
replies
81
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Problem installing ChAMP on a MacBook
ChAMP
updated 1 day ago by 3.9k • written 1 day ago by • 0
2
votes
3
replies
261
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package goseq seems to be not available on the latest version of R
goseq
updated 11 days ago by 50k • written 13 days ago by ▴ 20
0
votes
3
replies
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
votes
3
replies
8.5k
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SingleR Label.Ont
SingleR
updated 5 days ago by • 0 • written 8 months ago by • 0
0
votes
2
replies
817
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Job: Bioinformatics Laboratory Head in AI or machine learning (WEHI, Australia)
bioconductor artificialintelligence JobPosting machinelearning
written 8 months ago by 50k
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
250
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
8 days ago • updated 7 days ago Dylan.Sheerin • 0
0
votes
2
replies
146
views
How to make DGEList and design matrix by edgeR package
DGEList edgeR
28 days ago prity6459 • 0
2
votes
2
replies
270
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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 19 hours ago Matthew Thornton ▴ 360
1
vote
2
replies
107
views
Can log2cpm be used for proteomics data normalization?
metaMSdata
2 days ago • updated 1 day ago Daniel • 0
2
votes
2
replies
209
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OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 27 days ago by 65k • written 28 days ago by • 0
2
votes
2
replies
231
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
17 days ago Chris ▴ 10
0
votes
2
replies
237
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
27 days ago • updated 25 days ago catv • 0
1
vote
2
replies
285
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData
16 days ago • updated 15 days ago Yveto • 0
1
vote
2
replies
737
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
29 days ago • updated 20 days ago Patadù ▴ 10
0
votes
2
replies
944
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation wgcna network
updated 2 days ago by • 0 • written 17 months ago by • 0
2
votes
2
replies
265
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
9 days ago • updated 4 days ago zzrammal • 0
1
vote
2
replies
211
views
Improving the design matrices vignette in RNAseq123
RNAseq123
25 days ago • updated 10 days ago Lluís Revilla Sancho ▴ 730
192 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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@Maria Doyle[sexdolltech][1]Hosting EuroBioC provides an excellent opportunity to showcase Bioconductor and computational biology research …
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Dear Daniele, for which Ensembl release would you need the data? the most recent is 112, but if you used a different version before it wou…
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Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
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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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