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0
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14
views
gene Set with high AUC score but no cells assigned to cell type
AUCell
11 hours ago
gogeni5529
• 0
0
votes
0
replies
24
views
GOseq Probability Weight Function bad fit
goseq
11 hours ago
francesca
• 0
0
votes
1
reply
40
views
Sharing a collection of datasets in ExperimentHub
Bioconductor
updated 9 hours ago by
shepherl
4.2k • written 1 day ago by
Stephen Piccolo
▴ 600
0
votes
0
replies
63
views
DESeq2 for candidate gene analysis
Bioconductor
4 days ago
piffelpaff
• 0
0
votes
1
reply
56
views
Problem with viewGO(ref_path) in SpliceWiz
Bioconductor
SpliceWiz
4 days ago • updated 12 hours ago
jalte.jelsing
• 0
0
votes
0
replies
26
views
Problem with the TMB plot
Bioconductor
4 days ago
nayanajose
• 0
0
votes
3
replies
1.4k
views
problem for finding soft power for constructing network in WGCNA algorithm
RNA-seq
WGCNA package
soft power
written 7.2 years ago by
modarzi
▴ 10
0
votes
0
replies
56
views
After running samtools, the featureCounts command crashed.
RNASeqData
RNASeq
rnaseqGene
6 days ago
Rui
• 0
0
votes
6
replies
242
views
GO.db and others package Download failure
GO.db
Bioconductor
updated 5 days ago by
James W. MacDonald
68k • written 6 days ago by
Skyler
• 0
0
votes
0
replies
7
views
Spam:
Best Rehab Center In India | Luxury, Alcohol & Mental Health Care
COSMIC.67
6 days ago
Best Rehab Center
0
0
votes
2
replies
106
views
replace cat with message in glmTreat when lfc = 0
edgeR
glmTreat
updated 4 days ago by
Gordon Smyth
53k • written 8 days ago by
oliverd
• 0
0
votes
0
replies
29
views
Job:
Research and Service Group Leader positions in AI in Biology at EMBL
Bioconductor
7 days ago
Wolfgang Huber
★ 13k
0
votes
1
reply
53
views
Differential motif analysis
motifmatchr
updated 7 days ago by
James W. MacDonald
68k • written 7 days ago by
Marek Gierlinski
▴ 30
1
vote
3
replies
163
views
DESeq2 interactions
DESeq2
updated 8 days ago by
swbarnes2
★ 1.4k • written 9 days ago by
Michael
• 0
0
votes
0
replies
35
views
News:
Ensembl 115 has been released!
ensembl
ensembldb
biomaRt
8 days ago
Ensembl_Jorge
• 0
0
votes
0
replies
36
views
A problem occurs when running the monocle2
monocle
8 days ago
yuheng_yang
• 0
0
votes
0
replies
28
views
News:
Bioconductor 3.22 Release Schedule
Devel
Release
Bioconductor
8 days ago
shepherl
4.2k
1
vote
3
replies
175
views
readDNAStringSet with non DNA characters
Biostrings
8 days ago • updated 7 days ago
biomiha
▴ 20
0
votes
2
replies
135
views
readBam vs read_bam_insert_metrics
cfDNAPro
cfDNA
updated 8 days ago by
James W. MacDonald
68k • written 11 days ago by
rtrivedi1
▴ 10
1
vote
3
replies
241
views
How to construct a BSgenome object from a custom genome assembly using BSgenomeForge?
BSgenome
BSgenomeForge
updated 8 days ago by
James W. MacDonald
68k • written 11 days ago by
mat149
▴ 80
3
votes
14
replies
807
views
DESeq2 used with zinbwave weights - Differences on contrasts calculations
zinbwave
DESeq2
written 7 weeks ago by
Aurélie
• 0
5
votes
12
replies
604
views
Guidance on limma for pseudobulk scRNA-seq with multi-factor design
limma
RNASeq
scRNAseq
12 days ago • updated 6 hours ago
abaed
• 0
0
votes
0
replies
53
views
Questions about pseudo counts from RUVSeq
RUVSeq
12 days ago
Yuxiang
• 0
0
votes
1
reply
3.0k
views
Job:
Postdoctoral Research Position in Cancer Genomics at Dana-Farber Cancer Institute/Harvard University
cancer
computational biology
rnaseq
chipseq
Job
written 10.9 years ago by
gcyuan
• 0
0
votes
2
replies
139
views
3-factor DESeq2 trime-series analysis
time-series
DESeq2
13 days ago • updated 12 days ago
gogeni5529
• 0
0
votes
3
replies
243
views
Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
RUVSeq
DESeq2
updated 12 days ago by
Michael Love
43k • written 21 days ago by
yongjie.wang
• 0
0
votes
1
reply
247
views
Which of apeglm and ashr may be more appropriate for pseudobulked DESeq2 analysis of single-cell RNA-seq data?
apeglm
DESeq2
updated 15 days ago by
Michael Love
43k • written 29 days ago by
KS
• 0
0
votes
3
replies
153
views
A0A287BB68 not recognized as UNPROT key in org.Ss.eg.db using AnnotationDbi::select()
org.Ss.eg.db
AnnotationDbi
written 26 days ago by
Adam Munhall
• 0
0
votes
4
replies
246
views
voomLmFit fitted log-CPM values
limma
edgeR
updated 17 days ago by
Gordon Smyth
53k • written 18 days ago by
Lina
▴ 10
0
votes
0
replies
81
views
Extract snp information from genomic regions with biomaRt -> "oaries_snp"
biomaRt
updated 20 days ago by
James W. MacDonald
68k • written 20 days ago by
Jesus
• 0
1
vote
3
replies
238
views
ROAST compare results with complex design
limma
mroast
roast
CAMERA
written 21 days ago by
Jiahao Tian
• 0
0
votes
0
replies
5
views
Spam:
Exploring Robotic Hair Restoration Procedure
COSMIC.67
25 days ago
paseje6172
0
0
votes
1
reply
125
views
Length of 'dimnames' [1] not equal to array extent
SingleCellExperiment
singlecelle
scRNAseq
26 days ago • updated 19 days ago
Francesco Silvestro
• 0
0
votes
0
replies
76
views
News:
Course: Single-cell analysis with R/Bioconductor
SingleCellExperiment
SingleCell
SingleCellWorkflow
SingleCellData
26 days ago
Ludwig Geistlinger
▴ 70
3
votes
5
replies
970
views
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
DESeq2
updated 21 days ago by
James W. MacDonald
68k • written 27 days ago by
snijesh
▴ 200
0
votes
1
reply
288
views
News:
Bioconductor Board Nominations Open
TAB
Bioconductor
CAB
written 9 weeks ago by
shepherl
4.2k
2
votes
8
replies
497
views
Are voomByGroup and voomLmFit compatible?
limma
voomLmFit
voomByGroup
updated 20 days ago by
Gordon Smyth
53k • written 5 weeks ago by
richardallenfriedmanbrooklyn
▴ 30
0
votes
3
replies
1.2k
views
How to analyze Affy data, CEL files not available
affy
affy
written 18.6 years ago by
Bobby Prill
▴ 60
0
votes
1
reply
144
views
org.Ss.eg.db MAMDC4 maps to incorrect UNIPROT key
MAMDC4
org.Ss.eg.db
AnnotationDbi
written 4 weeks ago by
Adam Munhall
• 0
0
votes
0
replies
87
views
mzR-Rcpp compiler version issue
Rcpp
Perseus
mzR
4 weeks ago
bniego
• 0
0
votes
0
replies
95
views
Corrupted SQLite while trying to install PANTHER.db?
SQLite
PANTHER.db
4 weeks ago
Alan
• 0
0
votes
5
replies
513
views
HMP_2019_t2d data origin
curatedMetagenomicData
updated 4 weeks ago by
Levi Waldron
★ 1.1k • written 10 weeks ago by
Blan
• 0
0
votes
0
replies
87
views
Finding duplicated entries in GRangesList
GenomicRanges
4 weeks ago
Marco
• 0
17
votes
45
replies
12k
views
Can NanoString data be analyzed using DESeq2?
NanoString
Differential Expressed Genes Analysis
DESeq2
updated 28 days ago by
James W. MacDonald
68k • written 6.2 years ago by
lim6432
▴ 60
0
votes
0
replies
102
views
DESeq2 on non-RNASeq counts data
DESeq2
4 weeks ago
vs
• 0
0
votes
0
replies
96
views
sigDF object in sesame
sesame
sesameData
4 weeks ago
Ramiro
• 0
3
votes
4
replies
7.8k
views
Calculation of module membership in WGCNA
WGCNA
RNA-seq
ModuleMembership
Network
Hub gene
written 5.1 years ago by
Arindam
▴ 80
1
vote
9
replies
809
views
Using DESeq2 on single cell RNA Seq data of same cell type but different conditions that were pseudo bulked
DESeq2
scRNAseq
5 weeks ago • updated 4 weeks ago
Raya
• 0
0
votes
11
replies
465
views
Getting way too many DEGs with LRT for time-series RNA-seq!
TimeCourse
DESeq2
5 weeks ago • updated 4 weeks ago
Denise
• 0
3
votes
4
replies
330
views
p-adjusted values in multiple comparisons
StatisticalMethod
limma
RnaSeqSampleSizeData
updated 7 days ago by
Josh
• 0 • written 5 weeks ago by
ocanorocabayera
• 0
46,636 results • Page
1 of 933
Recent ...
Replies
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
by
abaed
• 0
Hello again @gordonsmyth, I've now applied the analysis using a more detailed annotation of cell types/clusters, which includes about 100 …
Answer: Sharing a collection of datasets in ExperimentHub
by
shepherl
4.2k
107 packages would be a lot! It is certainly possible (and recommended) to implement one package that utilizes ExperimentHub for controlli…
Comment: GO.db and others package Download failure
by
James W. MacDonald
68k
Also, you never need to use anything but `BiocManager::install` to install any package, which has the beneficial side effect of ensuring th…
Comment: GO.db and others package Download failure
by
James W. MacDonald
68k
Yes. Your packages have odd Y version numbers (where the version is X.Y.Z). That means they are devel packages (release versions have even …
Comment: GO.db and others package Download failure
by
Skyler
• 0
Am I using Bioc-devel?
Votes
Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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