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9
views
what should be the input for SingleR() automatic cell type annotation?
SingleR
1 hour ago
Yijing
• 0
0
votes
0
replies
19
views
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
views
Deseq contrast question
RNASeqData
DESeq2
5 hours ago
Hannah
▴ 10
0
votes
0
replies
28
views
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
ATpoint
★ 2.9k • written 1 day ago by
liuyang32201220
• 0
0
votes
0
replies
26
views
MAGECK MLE design matrix
mageck
MAGeCKFlute
1 day ago
Monika
• 0
0
votes
0
replies
34
views
mzTab-M in XCMS
xcms
mzTab-M
iterativehierarchicalprocessing
FBMN
3 days ago
Abrianna
• 0
0
votes
1
reply
81
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 2 days ago by
betterwound
• 0 • written 4 days ago by
abhisek001
• 0
0
votes
0
replies
33
views
plotGOTermGraph connects all subtrees to the root node
GO.db
GOstats
6 days ago
RuBBiT0
▴ 10
0
votes
0
replies
33
views
Positive beta-scores of essential genes in drug-treated cells
mageck
MAGeCKFlute
CrisprScreen
6 days ago
Monika
• 0
0
votes
0
replies
39
views
alpha1 in SAFFRON method in onlineFDR package
onlineFDR
8 days ago
lgomeso
• 0
0
votes
0
replies
49
views
Title in dba.plotProfile
DiffBind
8 days ago
agata17
• 0
2
votes
4
replies
165
views
BiocGenerics binary is outdated for macOS ARM
BiocGenerics
9 days ago
Michael Steinbaugh
▴ 90
0
votes
1
reply
72
views
Recount3: PCR duplicates
pcrduplicates
recount3
multimappingreads
updated 9 days ago by
ATpoint
★ 2.9k • written 9 days ago by
seline.natalie
• 0
0
votes
1
reply
98
views
Merge 2 accounts, or delete 1 account.
Bioconductor
ALL
updated 9 days ago by
shepherl
3.5k • written 9 days ago by
simone.tiberi
• 0
0
votes
0
replies
61
views
fgsea/clusterProfiler Packages for nCounter data enrichment analysis
NanoStringDiff
clusterProfiler
fgsea
10 days ago
pg45863
• 0
0
votes
0
replies
98
views
Error while performing DEXseq
DEXSeq
11 days ago
vipul14
• 0
0
votes
0
replies
52
views
Subsite info is possible for more studies
curatedMetagenomicData
13 days ago
Vitor Heidrich
• 0
0
votes
0
replies
50
views
WGCNA of two different cohorts study
DifferentialExpression
WGCNA
updated 4 days ago by
Michael Love
40k • written 13 days ago by
suphamon.j
• 0
2
votes
1
reply
120
views
WGCNA: many over and under-expressed features in modules of a signed network
WGCNA
wgcna_package
updated 8 days ago by
andres.firrincieli
▴ 50 • written 14 days ago by
hesse.sebastian
▴ 10
0
votes
0
replies
66
views
HiCDCPlus glm.fit error
HiCDCPlus
14 days ago
ehamrud
• 0
0
votes
0
replies
69
views
blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules
WGCNA
consensus
15 days ago
Levi
• 0
0
votes
0
replies
56
views
Fold values in Diffbind
DiffBind
15 days ago
bhandary.8590
• 0
1
vote
2
replies
178
views
Error: biomaRt has encountered an unexpected server error.
biomaRt
updated 7 days ago by
Mike Smith
★ 6.0k • written 15 days ago by
Yijing
• 0
0
votes
0
replies
51
views
Illumina global SNP screeing array
illuminaHumanv3.db
arrays
15 days ago
DH
• 0
1
vote
4
replies
218
views
Submitting BSgenome package for a new assembly
bsgenome
GenomicFeatures
package
updated 6 days ago by
Hervé Pagès
16k • written 15 days ago by
Manish
• 0
0
votes
2
replies
109
views
msa Installation failed - please help
Install
msa
15 days ago
Ido
• 0
0
votes
0
replies
69
views
'ZygosityPredictor's dependency 'datastructures' missing in R 4.3.0
ZygosityPredictor
updated 19 days ago by
Kevin Blighe
3.8k • written 20 days ago by
Marc
• 0
0
votes
2
replies
169
views
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
views
Help with Diffbind result
DiffBind
23 days ago • updated 22 days ago
Chris
• 0
0
votes
1
reply
109
views
ageData (minfi pipeline)
ageData
missMethyl
differentialvariability
minfi
updated 24 days ago by
Basti
▴ 720 • written 24 days ago by
Saanchi
• 0
0
votes
0
replies
75
views
IsoformSwitchAnalyzer
Isoform
IsoformSwitchAnalyzeR
26 days ago
Craig
• 0
0
votes
0
replies
55
views
How to get the class ID of patients using ConsensusClusterPlus
ConsensusClusterPlus
27 days ago
hsin hsiung
• 0
0
votes
0
replies
92
views
High Memory Usage when running FRASER's countRNAData
FRASER
27 days ago
jbendik
• 0
0
votes
4
replies
375
views
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
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 28 days ago by
James W. MacDonald
63k • written 28 days ago by
Esraa
• 0
0
votes
3
replies
236
views
Why is RNA-Seq library size not constant among samples?
RNA-Seq
sequencer
library_size
sequency_depth
multiplexing
offtopic
updated 28 days ago by
James W. MacDonald
63k • written 28 days ago by
FedeXander
• 0
0
votes
0
replies
70
views
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
Martin Morgan
25k • written 5 weeks ago by
Michael Steinbaugh
▴ 90
0
votes
0
replies
80
views
Getting the exon co-ordinates and location
exon
AnnotationHubData
5 weeks ago
mahima.g
• 0
0
votes
1
reply
149
views
WGCNA for one perturbation time series (pooled from two independent replicates)?
WGCNA
updated 5 weeks ago by
ATpoint
★ 2.9k • written 5 weeks ago by
Adam
• 0
0
votes
1
reply
102
views
custom annotations with annotatr
annotatr
5 weeks ago
luca.s
▴ 40
0
votes
0
replies
107
views
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
views
Volcano plot
limma
AffymetrixChip
5 weeks ago
e.gunaut
• 0
0
votes
2
replies
198
views
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
views
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
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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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