2
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3
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2.2k
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Keep getting this error "Warning: unable to access index for repository"?
CATALYST
updated 11 months ago by 16k • written 11 months ago by ▴ 20
4
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8
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2.2k
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Can we use rlog or vst data values in limma for differential expression analysis?
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updated 11 months ago by 50k • written 17 months ago by ▴ 20
3
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16
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DESeq2 - groups with biological replicates from the same patient
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updated 3 months ago by 3.9k • written 2.9 years ago by ▴ 10
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Why the LogFC and delta-beta value are different in ChAMP
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updated 11 weeks ago by • 0 • written 3.4 years ago by • 0
3
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12
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t.test to determine the P-value in DESeq2
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written 18 months ago by • 0
1
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5
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pd.mogene.2.0st Error Installing in R 3.1.2
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clusterProfiler - custom annotations
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updated 4 months ago by ★ 3.9k • written 16 months ago by • 0
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6
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Error when Installing BioConductor Package ('affy')
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updated 5 months ago by ★ 4.1k • written 17 months ago by • 0
3
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6
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Result from GSEA for non-model organism not as expected
clusterProfiler
updated 5 months ago by 65k • written 18 months ago by ▴ 10
4
votes
4
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Unlog transformed data in DESeq2
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updated 5 months ago by 50k • written 2.4 years ago by ▴ 10
0
votes
1
reply
2.1k
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Is it proper to compare two WGCNA matrixes if they were raised to different power (soft threshold)?
Network cluster WGCNA RNASeq
updated 9 months ago by 65k • written 9 months ago by • 0
4
votes
7
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2.1k
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should statmod be a dependency of limma and not a suggests?
limma
updated 9 months ago by 50k • written 7.9 years ago by • 0
1
vote
10
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2.1k
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Interprteting the phylogenomic profiles plot
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written 17 months ago by • 0
0
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2
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2.1k
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Creating a qPCRset object from a text file
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updated 6 months ago by • 0 • written 6.3 years ago by • 0
0
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11
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globaltest question
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written 17.7 years ago by ▴ 30
0
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2
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2.0k
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ChAMP::champ.norm Error in champ.BMIQ(beta[, x], design.v, sampleID = colnames(beta)[x], : task 1 failed - "only defined on a data frame with all…
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updated 6 months ago by • 0 • written 5.0 years ago by ▴ 20
0
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5
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2.0k
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How can I limit the number of displayed genes in heatplot
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updated 8 months ago by • 0 • written 16 months ago by • 0
15
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23
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The difference when using Limma compare between 3 conditions vs 2 conditions
limma
6 weeks ago • updated 12 days ago Chris • 0
0
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5
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Normalizing Affy Almac Xcel Array Data from CEL files
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written 10.4 years ago by ★ 13k
0
votes
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Error with phyloseq R package with Conda install
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written 7.5 years ago by • 0
2
votes
2
replies
2.0k
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humann2 output appropriate for EdgeR or DESeq2 analysis
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updated 8 months ago by • 0 • written 6.4 years ago by • 0
2
votes
6
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2.0k
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clusterProfiler for KEGG enrichment (non-model species) Over-Representation Analysis
KEGG clusterProfiler
updated 4 months ago by ★ 3.9k • written 14 months ago by ▴ 10
5
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3
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Cannot download GEOmetadb sqlite file
GEOmetadb
updated 3 months ago by • 0 • written 6.5 years ago by ▴ 10
2
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7
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How to generate custom annotation for rat genome rn6 in ChIPQC
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updated 4 months ago by • 0 • written 3.7 years ago by • 0
0
votes
14
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2.0k
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Error while preprocessing raw data from methylation array using minfi package
minfi
updated 3 months ago by • 0 • written 8 months ago by • 0
10
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11
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2.0k
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tximport error: vroom
tximport
updated 6 months ago by • 0 • written 7 months ago by ▴ 40
1
vote
1
reply
2.0k
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Help with error DiffBind
DiffBind
updated 9 months ago by ★ 5.2k • written 10 months ago by • 0
0
votes
4
replies
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Subtracting INPUT reads from ChIP read counts.
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updated 3 months ago by ★ 5.2k • written 7.9 years ago by • 0
4
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5
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time course microarray data ArrayExpress database
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updated 7 months ago by ▴ 40 • written 19 months ago by ▴ 20
1
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4
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ComBat Normalisation - data is integers and some floats, confused?!
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updated 6 months ago by • 0 • written 3.2 years ago by • 0
1
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1
reply
1.9k
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Tutorial: Update gene symbols in GeneSetCollection
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written 5.9 years ago by ▴ 170
5
votes
5
replies
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Archive location for Bioconductor packages
archive
updated 8 months ago by 3.9k • written 20 months ago by ▴ 20
3
votes
6
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Why NanoStringDiff package so slow?
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updated 6 months ago by • 0 • written 4.8 years ago by ▴ 50
2
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5
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Problem at champ.load
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updated 8 weeks ago by 65k • written 12 months ago by • 0
5
votes
6
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Questions about using training sets and WGCNA module eigengenes generated separately for Pigengene package
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6 months ago • updated 5 months ago kjngo ▴ 40
8
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13
replies
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Interpret plot from DiffBind
DiffBind
updated 11 months ago by ★ 5.2k • written 11 months ago by • 0
0
votes
5
replies
1.9k
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DESeq LRT test and construction of Co-expression network
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updated 11 months ago by • 0 • written 6.2 years ago by ▴ 30
0
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4
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1.9k
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how to save subsetted GDS file
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written 6.0 years ago by ▴ 30
1
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3
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1.9k
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DeSEQ 2 Error: some values in assay are negative
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11 months ago dania.khalid • 0
1
vote
3
replies
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Making MDS plot
plotMDS limma
updated 10 months ago by 50k • written 10 months ago by • 0
1
vote
3
replies
1.9k
views
enrichKEGG results for non-model organism
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updated 12 weeks ago by • 0 • written 23 months ago by • 0
1
vote
3
replies
1.9k
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DiffBind error: diffbind DESeq2 analysis has not been run for this contrast
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updated 4 months ago by ★ 5.2k • written 6.6 years ago by • 0
3
votes
1
reply
1.9k
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TwoSampleMR and ieugwasr
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updated 8 weeks ago by ▴ 10 • written 2.2 years ago by ▴ 90
11
votes
4
replies
1.9k
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LIMMA dupcor() function time issue.
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updated 7 months ago by 50k • written 5.3 years ago by • 0
4
votes
13
replies
1.8k
views
Speeding up of DelayedArray::write_block()
HDF5Array DelayedArray
updated 7 months ago by 16k • written 2.6 years ago by ▴ 10
1
vote
6
replies
1.8k
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Rsubread - Error on buildindex - big ref sequence
Rsubread
updated 9 months ago by ▴ 380 • written 4.2 years ago by • 0
0
votes
7
replies
1.8k
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error with champ.load
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updated 8 months ago by • 0 • written 4.1 years ago by • 0
3
votes
7
replies
1.8k
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Installing densvis on a Singularity container
densvis docker
updated 11 months ago by ▴ 160 • written 12 months ago by 65k
1
vote
7
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1.8k
views
Error using champ.import
ChAMP EPICv2
updated 25 days ago by • 0 • written 10 months ago by • 0
2
votes
7
replies
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Issue with GSVA using dgCMatrix
GSVA
updated 9 weeks ago by ▴ 10 • written 2.9 years ago by • 0
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