0
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0
replies
9
views
what should be the input for SingleR() automatic cell type annotation?
SingleR
1 hour ago Yijing • 0
0
votes
0
replies
19
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Can DESeq2 handle huge variations in sequencing depth among samples?
HugevariationsinsequencingDepth DESeq2
2 hours ago Gopinath • 0
0
votes
0
replies
15
views
Comparing DGE between datasets with uneven sample sizes using DESeq2
unevensamplesizes ComparingDGEresults DESeq2
4 hours ago reba.duncan • 0
1
vote
0
replies
19
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Deseq contrast question
RNASeqData DESeq2
5 hours ago Hannah ▴ 10
0
votes
0
replies
28
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Recommendation sought for differential exon usage of a single gene
isofor DEXSeq DifferentialSplicing
20 hours ago nick_brittain55 • 0
0
votes
1
reply
56
views
Several questions about the workflow using DESeq2 to process RNA data
DESeq2
updated 7 hours ago by ★ 2.9k • written 1 day ago by • 0
0
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0
replies
26
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MAGECK MLE design matrix
mageck MAGeCKFlute
1 day ago Monika • 0
0
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0
replies
34
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mzTab-M in XCMS
xcms mzTab-M iterativehierarchicalprocessing FBMN
3 days ago Abrianna • 0
0
votes
1
reply
81
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Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 2 days ago by • 0 • written 4 days ago by • 0
0
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0
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33
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plotGOTermGraph connects all subtrees to the root node
GO.db GOstats
6 days ago RuBBiT0 ▴ 10
0
votes
0
replies
33
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Positive beta-scores of essential genes in drug-treated cells
mageck MAGeCKFlute CrisprScreen
6 days ago Monika • 0
0
votes
0
replies
39
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alpha1 in SAFFRON method in onlineFDR package
onlineFDR
8 days ago lgomeso • 0
0
votes
0
replies
49
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Title in dba.plotProfile
DiffBind
8 days ago agata17 • 0
2
votes
4
replies
165
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BiocGenerics binary is outdated for macOS ARM
BiocGenerics
9 days ago Michael Steinbaugh ▴ 90
0
votes
1
reply
72
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Recount3: PCR duplicates
pcrduplicates recount3 multimappingreads
updated 9 days ago by ★ 2.9k • written 9 days ago by • 0
0
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1
reply
98
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Merge 2 accounts, or delete 1 account.
Bioconductor ALL
updated 9 days ago by 3.5k • written 9 days ago by • 0
0
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0
replies
61
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fgsea/clusterProfiler Packages for nCounter data enrichment analysis
NanoStringDiff clusterProfiler fgsea
10 days ago pg45863 • 0
0
votes
0
replies
98
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Error while performing DEXseq
DEXSeq
11 days ago vipul14 • 0
0
votes
0
replies
52
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Subsite info is possible for more studies
curatedMetagenomicData
13 days ago Vitor Heidrich • 0
0
votes
0
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50
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WGCNA of two different cohorts study
DifferentialExpression WGCNA
updated 4 days ago by 40k • written 13 days ago by • 0
2
votes
1
reply
120
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WGCNA: many over and under-expressed features in modules of a signed network
WGCNA wgcna_package
updated 8 days ago by ▴ 50 • written 14 days ago by ▴ 10
0
votes
0
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66
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HiCDCPlus glm.fit error
HiCDCPlus
14 days ago ehamrud • 0
0
votes
0
replies
69
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blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules WGCNA consensus
15 days ago Levi • 0
0
votes
0
replies
56
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Fold values in Diffbind
DiffBind
15 days ago bhandary.8590 • 0
1
vote
2
replies
178
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Error: biomaRt has encountered an unexpected server error.
biomaRt
updated 7 days ago by ★ 6.0k • written 15 days ago by • 0
0
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0
replies
51
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Illumina global SNP screeing array
illuminaHumanv3.db arrays
15 days ago DH • 0
1
vote
4
replies
218
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Submitting BSgenome package for a new assembly
bsgenome GenomicFeatures package
updated 6 days ago by 16k • written 15 days ago by • 0
0
votes
2
replies
109
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msa Installation failed - please help
Install msa
15 days ago Ido • 0
0
votes
0
replies
69
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'ZygosityPredictor's dependency 'datastructures' missing in R 4.3.0
ZygosityPredictor
updated 19 days ago by 3.8k • written 20 days ago by • 0
0
votes
2
replies
169
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No compilation on Windows y compilation on linux
Devel PackageType deve
20 days ago • updated 5 days ago Franck RICHARD • 0
0
votes
0
replies
108
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Help with Diffbind result
DiffBind
23 days ago • updated 22 days ago Chris • 0
0
votes
1
reply
109
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ageData (minfi pipeline)
ageData missMethyl differentialvariability minfi
updated 24 days ago by ▴ 720 • written 24 days ago by • 0
0
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0
replies
75
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IsoformSwitchAnalyzer
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26 days ago Craig • 0
0
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0
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55
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How to get the class ID of patients using ConsensusClusterPlus
ConsensusClusterPlus
27 days ago hsin hsiung • 0
0
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0
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92
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High Memory Usage when running FRASER's countRNAData
FRASER
27 days ago jbendik • 0
0
votes
4
replies
375
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BioCann repository index warning on Apple Silicon (Bioc 3.17 / R 4.3)
Annotation
28 days ago • updated 21 days ago Michael Steinbaugh ▴ 90
0
votes
1
reply
95
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Calculate RPKMs and Output proteins pass the cutoff into FASTA file ... Error in keepSeqlevels(anno, seqlevels(galn), pruning.mode = "coarse") : i…
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updated 28 days ago by 63k • written 28 days ago by • 0
0
votes
3
replies
236
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Why is RNA-Seq library size not constant among samples?
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updated 28 days ago by 63k • written 28 days ago by • 0
0
votes
0
replies
70
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dmrseq and polymorphisms
dmrseq
5 weeks ago giancarlo.castellano • 0
1
vote
11
replies
408
views
BiocParallel 1.33.12 binary has incorrect library linkage on macOS x86
BiocParallel
updated 4 weeks ago by 25k • written 5 weeks ago by ▴ 90
0
votes
0
replies
80
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Getting the exon co-ordinates and location
exon AnnotationHubData
5 weeks ago mahima.g • 0
0
votes
1
reply
149
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WGCNA for one perturbation time series (pooled from two independent replicates)?
WGCNA
updated 5 weeks ago by ★ 2.9k • written 5 weeks ago by • 0
0
votes
1
reply
102
views
custom annotations with annotatr
annotatr
5 weeks ago luca.s ▴ 40
0
votes
0
replies
107
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PLSDA : No model was built because the first predictive component was already not significant.
plsda
5 weeks ago MLF • 0
0
votes
0
replies
116
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Volcano plot
limma AffymetrixChip
5 weeks ago e.gunaut • 0
0
votes
2
replies
198
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Limma multi-group, nested analysis with aggregation
limma
5 weeks ago Jonathan • 0
0
votes
0
replies
86
views
How to speed up pileup from Rsamtools?
Rsamtools pileup
5 weeks ago alexandr.gopanenko ▴ 40
0
votes
1
reply
178
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Probe off-target prediction: Identifying short sequence matches - potentially with mismatches & indels - in a transcriptome
Microarray Alignment Biostrings
5 weeks ago sandmann.t ▴ 70
0
votes
0
replies
84
views
package ‘riboSeqR’ is not available for this version of R
Bioconductor riboSeqR
5 weeks ago Javier • 0
0
votes
1
reply
119
views
topGO() analysis of DMPs in missMethyl methylation analysis
DNAMethylation missMethyl Pathways
5 weeks ago Grace • 0
1,000 results • Page 1 of 20
Recent ...
Replies
Answer: multiple filters in biomaRt by RuBBiT0 ▴ 10
First, yes, one gene could be related to several GO ID, and the result is based on the annotation package you use. Second, could you pro…
Comment: Diffbind "No genome detected" by kyliecode • 0
Hi Dr. Stark, Thanks very much for your reply! The bam files were output from nf-core/chipseq pipeline and for some reason, they do not ha…
Answer: Discrepancy between DESeq2 files produced in Galaxy and R(RStudio) by Michael Love 40k
I guess that Galaxy may be using some kind of LFC shrinkage, but without seeing their code I wouldn't know for sure. Shrinkage generally…
Comment: TCGAbiolinks cannot find bcr_patient_barcode by Habil Zare ▴ 170
I checked your example with the devel version 2.29.6 on Bioc and it worked fine. Thanks for the fix!
Answer: error in ChAMP loading file by jenniferbrowngates • 0
I got a lot of information from this website about different topics which is beneficial for me too so I thank this site and also suggest a …
Votes
Answer: Using PEER to identify hidden confounders in RNA-seq data (not working)
Comment: Error: biomaRt has encountered an unexpected server error.
Comment: Interpret plot from DiffBind
Comment: Interpret plot from DiffBind
Comment: Interpret plot from DiffBind
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