3
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18
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3.0k
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News: List of Deprecated Packages for Bioc3.18
Deprecation devel Bioconductor Devel
10 months ago • updated 29 days ago shepherl 3.9k
7
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28
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Rsubread::featureCounts extremely slow on some annotations
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updated 3 months ago by 50k • written 9.2 years ago by ★ 7.9k
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742
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News: List of Deprecated Packages for Bioc3.19
Release Devel ExperimentData Software
11 weeks ago • updated 23 days ago shepherl 3.9k
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BAM files to Genomic Ranges object
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updated 5 months ago by • 0 • written 11.4 years ago by ▴ 280
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Cn.mops error: Error in if (sum(rds.counts) == 0) { : missing value where TRUE/FALSE needed
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updated 9 weeks ago by • 0 • written 6.3 years ago by ▴ 10
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limma, analysis on subset of data gives completely different results
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updated 6 weeks ago by 50k • written 9.8 years ago by ▴ 40
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updated 8 weeks ago by • 0 • written 9.0 years ago by ▴ 150
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Can I use EdgeR log2(cpm) instead of voom log2(cpm) to be analyzed as microarray data?
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written 7.5 years ago by ▴ 10
3
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Error: 'IdClusters'
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updated 11 months ago by ▴ 10 • written 15 months ago by • 0
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DESEq2 Paired samples Before and after treatment
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updated 12 weeks ago by 42k • written 7.9 years ago by ▴ 30
2
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object HPOGENE is not exported by namespace HPO.db
clusterProfiler HPO.db
updated 6 months ago by ▴ 50 • written 6 months ago by ▴ 30
0
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458
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DESeq2 filtering vs edgeR filtering
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9 weeks ago • updated 7 weeks ago fr8712ca-s • 0
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masigpro Error in terms.formula(formula, data = data) : '.' in formula and no 'data' argument
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updated 9 months ago by • 0 • written 9.0 years ago by ▴ 120
0
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5
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pathway finding software
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1
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3
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maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicatedVariants, : missing required fields from MAF: Chromosome
software error maftools tcgabiolinks
updated 8 weeks ago by ▴ 20 • written 6.6 years ago by ▴ 100
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11
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bug in cpg.annotate() and DMR.plot: bad defaults for what and arraytype arguments
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updated 3 months ago by ▴ 180 • written 7.1 years ago by ★ 2.0k
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Normalizing Affy Almac Xcel Array Data from CEL files
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Unable to install DESeq2
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updated 10 months ago by 65k • written 10 months ago by • 0
1
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9
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how to control age and gender effect in expression data using DESeq2
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10
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Interprteting the phylogenomic profiles plot
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1
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16
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error in ChAMP loading file
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updated 9 weeks ago by • 0 • written 18 months ago by • 0
2
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3
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TPM from STAR mapped counts
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updated 8 months ago by 50k • written 8 months ago by • 0
2
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Rsubread: subjunc() loads index repeatedly
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10 months ago • updated 9 months ago Gerhard Thallinger ▴ 180
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Problem about picking soft threshold power in WGCNA software
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written 7.2 years ago by ▴ 40
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mailman bugs
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21.3 years ago • updated 11 months ago Gordon Smyth 50k
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problem while retriving the genes by using p value and log2fc as conditions
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11 months ago sreeshmaraj72 • 0
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3
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extract rsids of SNPs using their genomic positions
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written 10 months ago by • 0
4
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13
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Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 7 months ago by 42k • written 8 months ago by • 0
10
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10
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SGSeq: moving toward diffex from SGSeq analysis
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updated 20 hours ago by ▴ 220 • written 6.7 years ago by ▴ 80
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How to process Nimblegen microarray .pair files to get normalized expression matrix
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Ensembl plants at annotationHub?
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updated 3 hours ago by • 0 • written 5.5 years ago by ★ 4.0k
2
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7
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EdgeR glmLRT vs glmQLFTest
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updated 8 months ago by • 0 • written 3.1 years ago by ▴ 20
0
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7
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Unable to install RefPlus - R=4.3.1, BiocManager=3.18
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44
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How to use bootRanges to bootstrap small RNA loci (nullranges package)
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updated 2 days ago by 42k • written 15 months ago by • 0
2
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readVcf(remoteFile, "hg19", "region") works on macos, fails on linux and in docker
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8
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CAGEr bug report: wrong consensus cluster results
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updated 10 months ago by ▴ 180 • written 17 months ago by ▴ 30
14
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1
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13
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unable to access index for repository
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updated 9 months ago by • 0 • written 17 months ago by • 0
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error with champ.load
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written 6.5 years ago by ▴ 10
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Microarray Limma Model fitting and DEG
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updated 7 weeks ago by 50k • written 7 weeks ago by • 0
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error message when I use the bsseq read.bismark command to read a genome wide cytosine report generated by bismark.
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updated 8 months ago by ▴ 740 • written 9 months ago by ▴ 20
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18
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Generation of QSEA TCGA 450K Human Methylation Calibration Dataset
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updated 4 months ago by ▴ 240 • written 7.1 years ago by ▴ 20
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annotation
written 8.9 years ago by • 0
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6
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LIMMA : design (1, 2, 3, 3 ) , I got EXCITING results, what could be the logic, since i have 2 replicates for 3rd group only ?
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updated 10 weeks ago by 50k • written 19.1 years ago by ★ 1.1k
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Import Salmon data with tximport and pool technical replicates
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written 9 months ago by • 0
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11
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globaltest question
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WGCNA documentation not available
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written 5 months ago by ▴ 10
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LIMMA: plotMDS
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1
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written 6.7 years ago by ▴ 180
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Background correction with neqc
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updated 6 months ago by 50k • written 12.4 years ago by ★ 13k
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Comment: Ensembl plants at annotationHub? by Daniele • 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools by BioinfGuru ▴ 30
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…
Answer: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by makala • 0
Thanks a lot!
Comment: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by Erik Wright ▴ 150
Thanks for notifying us of this broken link. It should be fixed on the Downloads page now. [1] [1]: http://www2.decipher.codes/Classificat…
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa by Matthew Thornton ▴ 360
So it turns out that if the count and the size are the same in 'GOstats", the odds ratio is 'inf'. These are causing the issue. Thank you!!
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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
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