1
vote
11
replies
1.5k
views
BiocParallel 1.33.12 binary has incorrect library linkage on macOS x86
BiocParallel
updated 12 months ago by 25k • written 12 months ago by ▴ 90
0
votes
1
reply
480
views
Calculate RPKMs and Output proteins pass the cutoff into FASTA file ... Error in keepSeqlevels(anno, seqlevels(galn), pruning.mode = "coarse") : i…
customProDB easyrun error mm10 Mus_musculus_Data
updated 12 months ago by 65k • written 12 months ago by • 0
0
votes
3
replies
856
views
Why is RNA-Seq library size not constant among samples?
RNA-Seq sequencer library_size sequency_depth multiplexing offtopic
updated 12 months ago by 65k • written 12 months ago by • 0
0
votes
0
replies
379
views
High Memory Usage when running FRASER's countRNAData
FRASER
11 months ago jbendik • 0
0
votes
0
replies
281
views
How to get the class ID of patients using ConsensusClusterPlus
ConsensusClusterPlus
11 months ago hsin hsiung • 0
0
votes
1
reply
672
views
Error calling GADEM from rGADEM package
rGADEM
updated 11 months ago by • 0 • written 18 months ago by • 0
0
votes
2
replies
1.2k
views
Pathway analysis using GAGE returns all NA values
gage rna-seq pathwayanalysis
updated 11 months ago by • 0 • written 3.5 years ago by • 0
0
votes
1
reply
1.4k
views
Keep getting NaN Values in GAGE analysis of KEGG pathways
KEGG GAGE NaN R DESeq2
updated 11 months ago by • 0 • written 5.5 years ago by • 0
0
votes
0
replies
376
views
IsoformSwitchAnalyzer
Isoform IsoformSwitchAnalyzeR
11 months ago Craig • 0
0
votes
1
reply
963
views
DMRfinder findDMRs.r Error - Argument is of length zero
DSS DMRcaller
updated 11 months ago by • 0 • written 21 months ago by • 0
0
votes
0
replies
499
views
Help with Diffbind result
DiffBind
11 months ago Chris • 0
0
votes
4
replies
1.2k
views
BioCann repository index warning on Apple Silicon (Bioc 3.17 / R 4.3)
Annotation
12 months ago • updated 11 months ago Michael Steinbaugh ▴ 90
0
votes
0
replies
311
views
'ZygosityPredictor's dependency 'datastructures' missing in R 4.3.0
ZygosityPredictor
updated 11 months ago by ★ 3.9k • written 11 months ago by • 0
0
votes
2
replies
586
views
msa Installation failed - please help
Install msa
11 months ago Ido • 0
0
votes
0
replies
366
views
Illumina global SNP screeing array
illuminaHumanv3.db arrays
11 months ago DH • 0
1
vote
0
replies
564
views
Fold values in Diffbind
DiffBind
11 months ago bhandary.8590 ▴ 20
0
votes
0
replies
428
views
blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules WGCNA consensus
11 months ago Levi • 0
0
votes
1
reply
790
views
SingleR error with multiple references
SingleR
updated 11 months ago by • 0 • written 17 months ago by • 0
0
votes
0
replies
294
views
Subsite info is possible for more studies
curatedMetagenomicData
11 months ago Vitor Heidrich • 0
0
votes
0
replies
396
views
Error while performing DEXseq
DEXSeq
11 months ago vipul14 • 0
0
votes
0
replies
839
views
fgsea/clusterProfiler Packages for nCounter data enrichment analysis
NanoStringDiff clusterProfiler fgsea
11 months ago pg45863 ▴ 10
2
votes
4
replies
610
views
BiocGenerics binary is outdated for macOS ARM
BiocGenerics
11 months ago Michael Steinbaugh ▴ 90
0
votes
0
replies
411
views
Title in dba.plotProfile
DiffBind
11 months ago agata17 • 0
2
votes
1
reply
510
views
WGCNA: many over and under-expressed features in modules of a signed network
WGCNA wgcna_package
updated 11 months ago by ▴ 50 • written 11 months ago by ▴ 10
0
votes
0
replies
270
views
alpha1 in SAFFRON method in onlineFDR package
onlineFDR
11 months ago lgomeso • 0
1
vote
2
replies
799
views
Error: biomaRt has encountered an unexpected server error.
biomaRt
updated 11 months ago by ★ 6.5k • written 11 months ago by • 0
1
vote
4
replies
748
views
Submitting BSgenome package for a new assembly
bsgenome GenomicFeatures package
updated 11 months ago by 16k • written 11 months ago by • 0
0
votes
0
replies
429
views
Positive beta-scores of essential genes in drug-treated cells
mageck MAGeCKFlute CrisprScreen
11 months ago Monika • 0
0
votes
0
replies
392
views
plotGOTermGraph connects all subtrees to the root node
GO.db GOstats
11 months ago RuBBiT0 ▴ 10
0
votes
2
replies
531
views
No compilation on Windows y compilation on linux
Devel PackageType deve
11 months ago Franck RICHARD • 0
1
vote
0
replies
475
views
WGCNA of two different cohorts study
DifferentialExpression WGCNA
updated 11 months ago by 41k • written 11 months ago by ▴ 20
0
votes
0
replies
409
views
mzTab-M in XCMS
xcms mzTab-M iterativehierarchicalprocessing FBMN
11 months ago Abrianna • 0
0
votes
0
replies
608
views
MAGECK MLE design matrix
mageck MAGeCKFlute
11 months ago Monika • 0
0
votes
0
replies
382
views
Recommendation sought for differential exon usage of a single gene
isofor DEXSeq DifferentialSplicing
11 months ago nick_brittain55 • 0
0
votes
0
replies
530
views
what should be the input for SingleR() automatic cell type annotation?
SingleR
11 months ago Yijing • 0
0
votes
2
replies
1.7k
views
ChAMP pipeline error (champ.import)
software error
written 5.1 years ago by • 0
0
votes
2
replies
497
views
Recount3: PCR duplicates
pcrduplicates recount3 multimappingreads
updated 11 months ago by • 0 • written 11 months ago by • 0
0
votes
1
reply
567
views
Recount3 data correspond to TCGA data
recount3
updated 11 months ago by • 0 • written 12 months ago by • 0
0
votes
1
reply
437
views
Error with IsoformSwitchAnalyzer: analyzePFAM
IsoformSwitchAnalyzeR
11 months ago Callum • 0
0
votes
1
reply
449
views
HiCDCPlus glm.fit error
HiCDCPlus
updated 11 months ago by • 0 • written 11 months ago by • 0
0
votes
1
reply
460
views
HiCDCPlus `construct_features` incompatible with BSgenome.Hsapiens.NCBI.T2T.CHM13v2.0 annotation
HiC-DC+ HiCDCPlus
updated 11 months ago by • 0 • written 17 months ago by • 0
0
votes
1
reply
404
views
HiCDCPlus extract_hic_eigenvectors() only works with larger bin sizes (> =250kb )?
HiCDCPlus
updated 11 months ago by • 0 • written 13 months ago by • 0
0
votes
1
reply
795
views
Error in loadFUN(x, seqname, ranges) : trying to load regions beyond the boundaries of non-circular sequence "chr2"
HiCDCPlus BSgenome.Hsapiens.UCSC.hg38
updated 11 months ago by • 0 • written 17 months ago by • 0
0
votes
1
reply
447
views
customProDB easyrun error in generating a custom protein database: Error in keepSeqlevels(anno, seqlevels(galn), pruning.mode = "coarse")
customProDB
10 months ago Esraa • 0
0
votes
0
replies
421
views
Issues setting background in STRINGdb
STRINGdb MSstats
10 months ago samsiljee • 0
0
votes
0
replies
430
views
Help with error running DiffBind
DiffBind
10 months ago Chris • 0
0
votes
0
replies
246
views
Can I plot values from LINCS level 4?
cmapR
10 months ago Alexandre • 0
0
votes
0
replies
278
views
Gene names not included on KEGGgraph plots
KEGGgraph
10 months ago hilarius_bookbinder • 0
1
vote
4
replies
1.1k
views
pathview - a species in KEGG pathway but not in 'korg'
pathview KEGG Oryza_sativa
10 months ago Jiyoung Lee • 0
0
votes
1
reply
522
views
Gene enrichment analysis
analysis R GOfuncR
updated 10 months ago by ▴ 730 • written 10 months ago by • 0
393 results • Page 1 of 8
Recent ...
Replies
Comment: SGSeq: moving toward diffex from SGSeq analysis by Sara • 0
Thank you for your response. I have another question about saving the sgvc result as a CSV file. I would appreciate your help, please. ``` …
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
I tried different block lengths first and considered 100000 to be ideal because of the almost similar inter-range distance. S1= bootRange…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k
The segmentation and block length are key parameters. We recommend for example blocks of length ~500kb. It would help if you would post yo…
Answer: Handling multiple differential expression comparisons by Michael Love 41k
It's typical that results are presented with each group having its own FDR control. So presenting each comparison with the adjusted p-va…
Comment: Too many significant genes when integrating gtex and tcga by ATpoint ★ 4.1k
These two datasets are from completely different experiments / batches. It is utterly meaningless to compare them. I would suggest comparat…
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Print Differentially Expressed Exons From Dexseq Results
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
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