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Votes
3
votes
3
replies
13k
views
How to fix 'long vectors not supported yet' error in R
r
updated 6 weeks ago by
Amruta
• 0 • written 5.3 years ago by
r.tor
• 0
8
votes
6
replies
509
views
DGE analysis with LIMMA
limma
updated 11 weeks ago by
Gordon Smyth
50k • written 11 weeks ago by
Amit
• 0
0
votes
3
replies
478
views
scran package: quickCluster and calculateSumFactors parallelization
BiocParallel
scran
updated 4 months ago by
ATpoint
★ 4.1k • written 4 months ago by
qwang178
• 0
2
votes
3
replies
365
views
seqlevelsStyle() not working
ensembldb
genomei
GenomeInfoDb
3 months ago
Kai Hu
▴ 70
4
votes
4
replies
463
views
edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 3 months ago by
James W. MacDonald
66k • written 4 months ago by
Geo
• 0
1
vote
7
replies
1.7k
views
enrichGOgradient color change
clusterProfiler
updated 9 weeks ago by
Guido Hooiveld
★ 4.0k • written 6 months ago by
inna.gur
• 0
4
votes
9
replies
496
views
Memory errors using read.bismark?
dmrseq
bsseq
5 weeks ago • updated 13 days ago
Juan Higareda
• 0
0
votes
3
replies
4.4k
views
The MicrobiotaProcess package performed lefse analysis and had a problem drawing the tree
MicrobiotaProcess
offspring.tbl_tree_item
updated 9 months ago by
Itscontentstop
• 0 • written 10 months ago by
fengjieli2021
• 0
2
votes
9
replies
1.2k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport
tximportData
DESeq2
10 months ago
Ndimensional
▴ 20
0
votes
4
replies
946
views
decontX (celda package)
decontX
celda
updated 6 months ago by
Marek Gierlinski
▴ 30 • written 6 months ago by
Shea
• 0
2
votes
3
replies
2.2k
views
Fail BiocManager::install(version='3.12')
BioManager
updated 9 weeks ago by
ATpoint
★ 4.1k • written 2.1 years ago by
liqidong52
▴ 20
1
vote
3
replies
3.4k
views
SRAdb: Error downloading sqlite files
sradb
written 6.6 years ago by
arielle
• 0
4
votes
7
replies
14k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq
R
edgeR
updated 8 months ago by
Gordon Smyth
50k • written 23 months ago by
Mohamed
▴ 30
3
votes
3
replies
9.6k
views
How to find rsID with biomaRt in R
biomaRt
updated 3 months ago by
James W. MacDonald
66k • written 3.2 years ago by
Federica
▴ 10
4
votes
4
replies
3.8k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler
GO
GO enrichment
genesetenrichment
updated 8 weeks ago by
jandrade
• 0 • written 6.4 years ago by
Huang, Lei [BSD] - CRI
▴ 20
9
votes
5
replies
5.1k
views
Differential expression analysis: Permutation Test
deseq2
limma
edger
permutation
updated 5 months ago by
Gordon Smyth
50k • written 8.2 years ago by
Radek
▴ 90
6
votes
10
replies
2.2k
views
overlapsAny for elements in GRangesList
granges
grangeslist
overlapsAny
updated 5 weeks ago by
Samuel Ahuno
• 0 • written 8.0 years ago by
maltethodberg
▴ 180
0
votes
2
replies
882
views
DiffBind dropping peaks in ATAC-seq data
DiffBind
ATACSeq
updated 9 months ago by
Malcolm Cook
★ 1.6k • written 10 months ago by
Nebat
• 0
3
votes
4
replies
293
views
Store output of matchPWM()
biostrings
Biostrings
19 days ago • updated 7 days ago
mat149
▴ 70
0
votes
3
replies
9.4k
views
SingleR Label.Ont
SingleR
updated 9 days ago by
Denis
• 0 • written 8 months ago by
saeed.khalili
• 0
0
votes
4
replies
246
views
Storing directories inside an ExperimentHub package?
ExperimentHub
5 weeks ago
Tim Barry
• 0
4
votes
14
replies
3.5k
views
Data input for aracne2regulon function in viper package
viper
updated 4 months ago by
YNPAN910
• 0 • written 4.8 years ago by
maya.kappil
▴ 30
3
votes
6
replies
23k
views
Deseq: What does "BaseMean" mean?
deseq2
updated 4 months ago by
kledo577
• 0 • written 5.7 years ago by
183227851
• 0
5
votes
6
replies
888
views
ASpli checks fail on Linux due to missing dependency to statmod
ASpli
updated 9 months ago by
Gordon Smyth
50k • written 9 months ago by
martin.grigorov
▴ 10
1
vote
3
replies
444
views
Cross-species analysis - how to compute the mid parent value?
DESeq2
limma
edgeR
DifferentialExpression
written 3 months ago by
pl23
• 0
5
votes
9
replies
2.5k
views
edgeR: Should there be a normalization step for CRISPR screens? How to deal with bottlenecked screens?
edger
calcnormfactors
updated 9 months ago by
Novice_cam
• 0 • written 6.5 years ago by
knaxerova
▴ 10
2
votes
8
replies
2.3k
views
Error in DGEList(counts = cnt, group = group) : non-numeric values found in counts
edgeR
13 months ago • updated 11 months ago
Luis
• 0
10
votes
8
replies
4.0k
views
conumee error: query intensities not given for all probes.
conumee
updated 4 months ago by
Mingkee
• 0 • written 6.9 years ago by
yura.grabovska
▴ 30
1
vote
8
replies
1.6k
views
Whether to build DESeq2 model with all data and then contrast groups or subset groups first, build model and then contrast?
DifferentialExpression
DESeq2
written 11 months ago by
sean.mccutcheon
• 0
0
votes
5
replies
1.7k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 13 months ago by
mauricio.microbiol
• 0
0
votes
4
replies
293
views
DEG with low counts
DESeq2
updated 4 weeks ago by
Michael Love
42k • written 5 weeks ago by
Rajat
• 0
1
vote
3
replies
361
views
Dispersion estimation step is very slow with latest DESeq2 and glmGamPoi
DESeq2
glmGamPoi
11 weeks ago • updated 10 weeks ago
I-Hsuan Lin
▴ 10
0
votes
9
replies
878
views
How long does it usually take to complete dream() from start to finish?
variancePartition
mixedmodel
dream
9 months ago
hayleyw
• 0
1
vote
4
replies
762
views
MDS plot edgeR
edgeR
updated 8 months ago by
Gordon Smyth
50k • written 8 months ago by
jbono
▴ 10
6
votes
19
replies
2.6k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 20 days ago by
Sey R.
• 0 • written 4.6 years ago by
hsbio
▴ 10
0
votes
4
replies
223
views
flowStats Search Error
flowStats
updated 4 weeks ago by
shepherl
3.9k • written 5 weeks ago by
tholmes
• 0
4
votes
6
replies
601
views
Merging of Human and Mouse SingleCellExperiment Objects Error
SingleCellExperiment
4 months ago
Dario Strbenac
★ 1.5k
1
vote
7
replies
1.3k
views
Diffbind "No genome detected"
DiffBind
updated 5 months ago by
James W. MacDonald
66k • written 11 months ago by
kyliecode
• 0
15
votes
17
replies
1.3k
views
Why p value inconsistent when using different number of pathway score?
limma
4 weeks ago • updated 19 days ago
Chris
▴ 10
6
votes
12
replies
5.1k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 28 days ago
shepherl
3.9k
6
votes
9
replies
874
views
biomaRt has encountered an unknown server error.
biomaRt
host
useEnsembl
updated 3 months ago by
alexander3
• 0 • written 3 months ago by
Amparo
• 0
1
vote
2
replies
350
views
Impute does not work
impute
12 weeks ago • updated 11 weeks ago
Laura
• 0
5
votes
18
replies
7.6k
views
Install DESeq2 problem for macbook pro M1 Max
Bioconductor
Install
DESeq2
updated 5 months ago by
picasa1983
• 0 • written 2.3 years ago by
Victor
• 0
0
votes
4
replies
3.2k
views
Problems with FLOWAI
flowAI
written 3.1 years ago by
msoares
• 0
0
votes
2
replies
505
views
EdgeR FTest
edgeR
updated 9 months ago by
Gordon Smyth
50k • written 9 months ago by
nawaz.u.toyama
• 0
2
votes
6
replies
3.0k
views
DESeq2 Dispersion Per Condition
deseq2
updated 10 months ago by
adi.rotem
• 0 • written 8.1 years ago by
dsg16
▴ 20
0
votes
2
replies
652
views
Fluidigm Data Batch Correction
sva
limma
updated 10 months ago by
Gordon Smyth
50k • written 10 months ago by
Khushbu
• 0
4
votes
5
replies
343
views
Method to find pathways different between 2 groups
fgsea
GSVA
CAMERA
15 days ago • updated 5 days ago
Chris
▴ 10
0
votes
4
replies
2.7k
views
Error using Bsmooth.tstat due to NAs
Coverage
bsseq
updated 6 months ago by
Adam
• 0 • written 9.7 years ago by
Guest User
★ 13k
1
vote
3
replies
916
views
Problem in running DESeq from expected count data of Transcriptome by Trinity followed by RSEM
Tissue
Spati
RSEM
deno
DEseq2
updated 11 months ago by
lauryfriese932
• 0 • written 12 months ago by
shashank
• 0
1,000 results • Page
3 of 20
Recent ...
Replies
Answer: Errors in chromosome annotation-biomaRt
by
James W. MacDonald
66k
If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …
Comment: Help with ENmix readidat
by
James W. MacDonald
66k
Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …
Comment: LRT, more than two conditions and pairwise comparisons
by
James W. MacDonald
66k
In that case, probably easiest to subset to the groups being compared.
Comment: Help with ENmix readidat
by
minardsmitha
▴ 10
Did you figure this out? I have the same issue.
Comment: LRT, more than two conditions and pairwise comparisons
by
boczniak767
▴ 720
Thank you for response, apparently I still don't know much about statistics. In fact I want to campare time-profiles [and the LRT has been …
Votes
Comment: LRT, more than two conditions and pairwise comparisons
Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
Comment: DESeq2- Mysterious interaction suppresses DEGs
Answer: DESeq2- Mysterious interaction suppresses DEGs
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