0
votes
31
replies
4.3k
views
Error in find DEXSeq package
deseq dexseq
9.0 years ago engr.yahya602 • 0
1
vote
21
replies
5.1k
views
Warning: unable to access index for repository https://bioconductor.org/packages/3.11/data/annotation/bin/macosx/contrib/4.0
BiocManager
written 3.9 years ago by ▴ 60
34
votes
21
replies
14k
views
DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
deseq2
9.6 years ago • updated 19 months ago Michael Love 41k
0
votes
21
replies
2.8k
views
How to use DECIPHER to design group-specific primers
Decipher
4.0 years ago hoonhuiyi • 0
0
votes
18
replies
5.8k
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WGCNA error in network construction ?
microarray rnaseq
7.1 years ago m.azhar ▴ 10
0
votes
16
replies
3.1k
views
Rgraphviz installation fails
rgraphviz
6.7 years ago Giovanni Calice ▴ 160
0
votes
16
replies
4.3k
views
Error while using buildindex for human genome
rsubread buildindex fasta alignment
5.5 years ago writetoroopali • 0
4
votes
15
replies
6.2k
views
mzR installation error: "unable to load shared object"
mzR installation
8.8 years ago Eugene • 0
0
votes
15
replies
2.7k
views
rlog not found
rlog rlog transformation
6.0 years ago crowsreign42 • 0
2
votes
15
replies
643
views
Problems with enrichGO
clusterProfiler enrichGO
updated 10 weeks ago by 41k • written 10 weeks ago by • 0
0
votes
14
replies
2.2k
views
Path to file in windows
bioconductor R windows diffbind
updated 7.0 years ago by ▴ 650 • written 7.0 years ago by • 0
0
votes
14
replies
1.7k
views
Error while opening Mart with biomaRt package
software error ensembl biomart
4.4 years ago loicborcard01 • 0
0
votes
14
replies
2.0k
views
Trouble downloading dada2
dada dada2
14 months ago elliottchon97 • 0
2
votes
13
replies
14k
views
Issues connecting with R 3.2.2 to source("http://bioconductor.org/biocLite.R")
spade
8.5 years ago frostbite907 • 0
5
votes
13
replies
4.1k
views
Getting error
enrichplot clusterProfiler org.Hs.eg.db
updated 2.1 years ago by ▴ 40 • written 2.1 years ago by • 0
2
votes
13
replies
1.9k
views
Found gaps in scan time of file : cut scantime-vector at NA seconds. Error: BiocParallel errors element index: 1, 2, 3, 4, 5, 6 first error: argu…
xcms adjustRtime parameters scantime error biocparallel error
4.6 years ago abrsoule ▴ 30
6
votes
12
replies
1.7k
views
Error when loading DMRcate
DMRcate
14 months ago Bazingastats • 0
1
vote
12
replies
4.5k
views
WGCNA: correlations module-traits, and module membership-gene significance
WGCNA co-expression analysis gene significance module membership module-trait relationship
updated 22 months ago by ▴ 10 • written 4.6 years ago by ▴ 30
1
vote
12
replies
3.8k
views
Problem with summarizeOverlaps function
genomicalignments read counting
8.7 years ago kgorczak ▴ 10
1
vote
12
replies
2.9k
views
readVcf does not recognize tabix index
VariantAnnotation readvcf tabix
updated 3.1 years ago by 6.7k • written 3.1 years ago by • 0
1
vote
12
replies
1.2k
views
Taking much longer time for same script after R upgrade to 4.0
R
3.8 years ago hsiowa2 ▴ 20
0
votes
11
replies
2.0k
views
Problem in subtracting ChIP Seq experiment with the input using ChIPSeqSpike
chipseq ChIPSeqSpike
updated 3.2 years ago by • 0 • written 3.3 years ago by • 0
2
votes
11
replies
6.0k
views
biomaRT connexion problem make failed my unit tests
biomaRt Peer's Certificate Ensembl
updated 3.2 years ago by ★ 6.5k • written 3.6 years ago by • 0
0
votes
11
replies
2.9k
views
Hello, I'm having trouble in installing Limma package and this is what Im getting
limma
updated 3.1 years ago by ★ 3.9k • written 3.1 years ago by • 0
2
votes
11
replies
5.4k
views
Error: cannot allocate vector of size ...MB
limma
8.3 years ago fahime.falahi • 0
3
votes
11
replies
3.5k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts Rsubread Subread
2.0 years ago • updated 24 months ago Sarah_piggy ▴ 10
5
votes
11
replies
2.7k
views
Error while installing Phyloseq using biocLite
bioclite phyloseq install error
5.5 years ago khp ▴ 30
2
votes
11
replies
7.1k
views
ClusterProfiler enrichGO function leads to different enrichment results in different computers, while the code and gene list keep same
clusterProfiler
2.3 years ago liuzhy ▴ 10
0
votes
11
replies
2.1k
views
rsbml fails to compile on Linux due to ParseMessage.h undetected with libSBML 5
rsbml compilation error configure
7.4 years ago zeb • 0
1
vote
11
replies
1.4k
views
BiocParallel 1.33.12 binary has incorrect library linkage on macOS x86
BiocParallel
updated 11 months ago by 25k • written 11 months ago by ▴ 90
0
votes
11
replies
4.3k
views
Examples from keggList in KEGGREST don't all work
software error keggrest
8.1 years ago Bryan Hanson • 0
2
votes
11
replies
2.0k
views
RBGL installation error
rbgl
8.0 years ago Julian Gehring ★ 1.3k
14
votes
10
replies
3.6k
views
Error when trying to preprocessReads() : "Error: logical subscript contains NAs"
systempiper
5.4 years ago Deleted ▴ 70
2
votes
10
replies
1.1k
views
Accounting for Batch effect reduces DEGs drastically
DESeq2
5 months ago rohitsatyam102 ▴ 20
1
vote
10
replies
2.7k
views
Building mzR package under docker fails
mzR docker debian centos rocker
8.5 years ago mjmg • 0
0
votes
10
replies
2.0k
views
behaviour of findOverlaps on GRangesList object
findOverlaps grangeslist GenomicRanges
6.8 years ago lovro0 ▴ 10
2
votes
10
replies
6.0k
views
Install older specific version from an R package that is on the Bioconductor Repository
Bioconductor biocLite R packages oldversion
8.4 years ago svlachavas ▴ 830
0
votes
10
replies
1.8k
views
Phyloseq to metagenomeSeq
limma metagenomeSeq
4.9 years ago Jitendra ▴ 10
0
votes
10
replies
2.0k
views
Ability to use a particular package via Docker
Docker flowcore dockerfile
7.6 years ago jordan.xanthopoulos • 0
2
votes
10
replies
2.1k
views
DEseq normalization Small RNA-seq data using rRNA
deseq2 normalization smallrna ribosomal rna
7.5 years ago mosharrofgeb ▴ 10
0
votes
9
replies
1.7k
views
Volcano plot non-numeric argument error
volcano plot edgr
7.2 years ago elena.capel ▴ 10
0
votes
9
replies
1.4k
views
summarizeOverlaps bplapply error in DeSeq2 pipeline
summarizeOverlaps R GenomicAlignments
updated 4.9 years ago by 25k • written 4.9 years ago by • 0
3
votes
9
replies
2.8k
views
Create object "Go3AnnDbBimap" and include it in a org.Xx.eg.db package to use with goProfiles and goTools
goprofiles AnnotationForge Bimap GO
9.6 years ago artur ▴ 80
4
votes
9
replies
7.8k
views
Upper triangular matrix heatmap using pheatmap package
pheatmap
8.3 years ago Deepak Tanwar ▴ 10
0
votes
9
replies
2.3k
views
Question about Agilent microarray data measurement
Agilent limma scan.upc microarray
7.5 years ago Maximilian ▴ 10
1
vote
9
replies
3.0k
views
Dotplots for differential gene expression data ?
clusterprofiler
3.8 years ago sunnykevin97 • 0
2
votes
9
replies
7.5k
views
Multiple alignments (multi-mapped reads) and DESeq/edgeR pipeline
deseq deseq2 edger tophat bowtie
8.9 years ago ysdel ▴ 40
1
vote
9
replies
2.4k
views
Removing batch effects from microarray data based on only a subset of samples
limma removebatcheffect() ComBat microarray
6.2 years ago jaro.slamecka ▴ 140
0
votes
9
replies
2.2k
views
problem using >3 clusters with Quasr
quasr parallel
updated 8.2 years ago by 25k • written 8.2 years ago by ▴ 90
0
votes
9
replies
1.6k
views
Unable to find solution: low coverage
PureCN fatal error no solution
5.9 years ago twtoal ▴ 10
1,000 results • Page 1 of 20
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Answer: minfi::read.metharray.exp by Basti ▴ 770
Could you show `list.files("~/Users/clarachretienneau/Desktop/clock epigenetic/PJ1209132_ScanData")` ? There may be a problem related to th…
Comment: DESeq2 - dispersion estimation when there is none by WardDeb • 0
Thank you for the pointers, I'll revert back again to the method section of the paper. As for the negative relationship of the estimated di…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function by Gayatri • 0
Hello James, How to generate the db? By running the makeOrgPackageFromNCBI() command? I have tried doing that, first by just deleting the …
Answer: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param by Tim Peters ▴ 170
Hi Jose and Russ, Apologies to Jose for not seeing this earlier. Sometimes the loess smoother in the bottom panel will throw this error …
Comment: Trying to use enrichGO by fernanda.backsouza • 0
Sure, I changed it but still NULL G0 <- enrichGO( gene = ortologos_filtrados$Gene.ID, OrgDb = org.Cs.eg.db, keyType = "ENTREZID",…
Votes
Answer: DESeq2 - dispersion estimation when there is none
Comment: Cannabis and KEGGgraph
Comment: Cannabis and KEGGgraph
Answer: Cannabis and KEGGgraph
Answer: Differentially expressed genes in monocle pseudotime
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