0
votes
3
replies
291
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A ComBat-seq issue: the covariates are confounded
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updated 4 weeks ago by ▴ 850 • written 5 weeks ago by • 0
0
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0
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137
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Warning while loading DEP package
DEP
updated 4 weeks ago by 3.9k • written 4 weeks ago by • 0
1
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2
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183
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Error in champ.load(): The following specified files do not exist
ChAMP
5 weeks ago • updated 4 weeks ago Sherin • 0
0
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1
reply
113
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Input Question for deseq.r
RSeqAn
updated 4 weeks ago by ★ 4.1k • written 5 weeks ago by • 0
1
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7
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1.9k
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ChAMP EPICv2
updated 5 weeks ago by • 0 • written 10 months ago by • 0
0
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0
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95
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Enzyme Engineering
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5 weeks ago bocchemistry • 0
0
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0
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109
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Syntaxt Error in IsorcorrectoR package with Molecule Info File
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5 weeks ago Maliha Tabassum • 0
0
votes
1
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138
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what is the sampleFiles
chipseq
updated 5 weeks ago by 66k • written 5 weeks ago by • 0
2
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2
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196
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[DiffBind] Obtaining normalization factors
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5 weeks ago Henry ▴ 10
0
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0
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109
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5 weeks ago Virangika • 0
0
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0
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86
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[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
5 weeks ago Henry ▴ 10
0
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1
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154
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Deseq2 Rlog transformation
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updated 5 weeks ago by ★ 4.1k • written 5 weeks ago by • 0
0
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1
reply
208
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compareCluster dotplot: how to modify the genesets order
DOSE enrichplot clusterProfiler
updated 5 weeks ago by ★ 4.0k • written 6 weeks ago by • 0
0
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0
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107
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Cannot use `readVcf()` on a file created with `writeVcf()`
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5 weeks ago Stevie Pederson • 0
0
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1
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202
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DESeq2 gives an error and R crashes
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6 weeks ago • updated 5 weeks ago Shefali • 0
3
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6
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319
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Surrogate variable analysis for paired RNA seq experiment
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5 weeks ago nhaus ▴ 40
0
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0
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161
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LearnTaxa with custom Silva
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6 weeks ago Eryn • 0
0
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0
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99
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6 weeks ago Dennis • 0
0
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1
reply
369
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Gene names from Matrix
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updated 6 weeks ago by ▴ 730 • written 7 months ago by • 0
0
votes
0
replies
133
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ggtree tip label position (depth)
ggtree
6 weeks ago Roope • 0
0
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1
reply
529
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Cibersort phenotype file
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2
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6
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486
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How to make boxplot with pairwise and overall p value from Limma
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6 weeks ago Chris ▴ 10
0
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1
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147
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Granges regionCounts not returning the expected number of entries
methylKit
6 weeks ago Modoc Kesner ▴ 10
0
votes
1
reply
564
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CopywriteR output
CopywriteR
updated 6 weeks ago by • 0 • written 2.6 years ago by • 0
0
votes
2
replies
319
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Error in if (nrow(peaks) > 0) { : argument is of length zero Calls: CopywriteR ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution h…
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7 weeks ago • updated 6 weeks ago fer_talavera • 0
0
votes
0
replies
165
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Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
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6 weeks ago andromeda • 0
0
votes
0
replies
118
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flowDensity on a flowset
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6 weeks ago fredrikwallberg • 0
0
votes
0
replies
107
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DMRcate error need at least two non-NA values to interpolate
DNAMethylation DMRcate
7 weeks ago Macsue • 0
0
votes
1
reply
177
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No output from read.bismark with bismark cov.files
bsseq methylation
updated 7 weeks ago by 66k • written 7 weeks ago by • 0
0
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7
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453
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Internet connection for Bioconductor packages in Rstudio in Iran...
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7 weeks ago needNGS • 0
0
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3
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346
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Statistical test
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1
vote
5
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375
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fgsea fork
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updated 7 weeks ago by 66k • written 7 weeks ago by • 0
0
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0
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127
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How to extract the coordinate of dba.plotPCA?
DiffBind PCA
7 weeks ago feather-W • 0
0
votes
0
replies
126
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PCA plot for normalized counts using Diffbind
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7 weeks ago Ankit ▴ 20
0
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0
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113
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7 weeks ago Pierre Lindenbaum ▴ 10
1
vote
3
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297
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miRTarRnaseq library
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updated 8 weeks ago by ▴ 10 • written 9 weeks ago by • 0
0
votes
1
reply
211
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Help with identifying genes mapped to KEGG pathway using pathview
pathview
updated 8 weeks ago by ★ 4.0k • written 9 weeks ago by • 0
1
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1
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278
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FCS3.2 reading
flowWorkspace flowCore CytoML
updated 8 weeks ago by ▴ 350 • written 3 months ago by ▴ 30
3
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3
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462
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Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
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updated 8 weeks ago by ▴ 160 • written 8 weeks ago by • 0
0
votes
2
replies
592
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ageData (minfi pipeline)
ageData missMethyl differentialvariability minfi
updated 8 weeks ago by • 0 • written 12 months ago by • 0
0
votes
0
replies
146
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Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals GenomicRanges
8 weeks ago gshweta95 • 0
2
votes
1
reply
241
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Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
updated 8 weeks ago by ★ 4.0k • written 8 weeks ago by ▴ 10
0
votes
2
replies
303
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Error in msaFun Cannot open input file. No alignment!
msa
written 9 weeks ago by ▴ 30
0
votes
0
replies
125
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Can i retrieve domain information from PANTHER ID's using PANTHER.db ?
PANTHER.db
8 weeks ago nromerov • 0
1
vote
3
replies
280
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cBioPortalData loads empty z-score expression table
cBioPortalData
updated 8 weeks ago by 700 • written 8 weeks ago by • 0
1
vote
4
replies
325
views
EDAseq to normalise for both gene-length and GC-content
norma EDASeq EDA Normalization
9 weeks ago samuel.channon • 0
0
votes
0
replies
145
views
crlmm: CDF for Infinium Global Diversity Array By Illumina
globaldiversityarray cdf crlmm
9 weeks ago mayra.haedo • 0
0
votes
0
replies
129
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Macsquant FCS in read.FCS & opencyto
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9 weeks ago taylor.witte • 0
0
votes
0
replies
156
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Multifactor analysis in DiffBind
DiffBind multifactoranalysis
9 weeks ago erbrocato • 0
1
vote
2
replies
322
views
Extracting genomic sequences using agat and bedtools yields different results
MAST
updated 9 weeks ago by ★ 4.1k • written 9 weeks ago by • 0
1,000 results • Page 2 of 20
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Comment: Not able to install any Bioconductor 3.18 package [unable to access index] by mgdrnl • 0
I solved the problem installing the latest R version (4.4.0)
Answer: Get gene symbols for a set of hg19 coordinates by ATpoint ★ 4.1k
Simply download a GTF file (for example from GENCODE) matching the current genome and/or annotation version you are using in your project a…
Comment: Not able to install any Bioconductor 3.18 package [unable to access index] by ATpoint ★ 4.1k
Try the mirror suggestion for now: https://support.bioconductor.org/p/9153734/#9153755
Comment: unable to access bioconductor packages - qvalue installation failed... by ATpoint ★ 4.1k
Seems to be a general problem at the moment, can reproduce. The the mirror suggestion here: https://support.bioconductor.org/p/9153734/#915…
Comment: Running ENmix with mouse methylation manifest: readidat error - Error in readman by Karosham.Reddy • 0
Thank you for the suggestion the ENmix version is using is ENmix_1.38.01. I tried your suggested code, R identified the idat files but sti…
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Comment: recount3 problem downloading data from source sra
Not able to install any Bioconductor 3.18 package [unable to access index]
unable to access bioconductor packages - qvalue installation failed...
Not able to install any Bioconductor 3.18 package [unable to access index]
can't open mghp.osn.xsede.org
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