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5
votes
8
replies
3.9k
views
Problem about picking soft threshold power in WGCNA software
wgcna
rnaseq
written 7.2 years ago by
panagiotis.mokos
▴ 40
0
votes
17
replies
3.4k
views
What causes this DESeq2 error at "fitting model and testing"?
deseq2
differential expression
error
updated 11 months ago by
snow34
• 0 • written 6.6 years ago by
ap3637
• 0
1
vote
5
replies
2.2k
views
pd.mogene.2.0st Error Installing in R 3.1.2
oligo
microarray
r
bioconductor
written 9.2 years ago by
chandlerjd58
▴ 10
2
votes
2
replies
398
views
"Details" section for specific software packages
Website
updated 6 months ago by
Mike Smith
★ 6.5k • written 6 months ago by
Justin
• 0
1
vote
3
replies
1.9k
views
Making MDS plot
plotMDS
limma
updated 10 months ago by
Gordon Smyth
50k • written 10 months ago by
liujy4
• 0
2
votes
3
replies
2.2k
views
Keep getting this error "Warning: unable to access index for repository"?
CATALYST
updated 11 months ago by
Hervé Pagès
16k • written 11 months ago by
Hyoann
▴ 20
0
votes
18
replies
2.5k
views
problem installing ENmix package
ENmix
Bioconductor
rtracklayer
written 3.2 years ago by
lea
• 0
0
votes
2
replies
236
views
WGCNA: analysis of complex trait associations with regressions
Regression
WGCNA
6 weeks ago • updated 5 weeks ago
w.cookson
• 0
0
votes
5
replies
9.3k
views
tximport all(file.exists(files)) is not TRUE
bioconductor
tximport
rnaseq
R
updated 7 weeks ago by
Eva
• 0 • written 7.6 years ago by
ctl
• 0
1
vote
3
replies
902
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
8
votes
7
replies
1.8k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2
glmGamPoi
DEXSeq
updated 10 months ago by
alexandresegers
▴ 20 • written 18 months ago by
jeremymsimon
▴ 20
4
votes
9
replies
1.3k
views
DittoDimPlot errror: Cannot find 'NA' in this Seurat object
dittoSeq
updated 8 months ago by
dbunis
▴ 10 • written 8 months ago by
nina.hahn
▴ 10
1
vote
3
replies
3.3k
views
SRAdb: Error downloading sqlite files
sradb
written 6.5 years ago by
arielle
• 0
0
votes
2
replies
564
views
Heat Map
ColData
pheatmap
DESeq2
written 10 months ago by
dania.khalid
• 0
4
votes
4
replies
3.4k
views
Best way to handle tags of bam files
GenomicAlignments
bam
Rsamtools
written 3.2 years ago by
changxu.fan
▴ 20
0
votes
2
replies
851
views
Error: insufficient numeric precision during Log fold change shrinkage with apeglm
apeglm
updated 8 months ago by
Michael Love
42k • written 8 months ago by
Juan Pablo
• 0
0
votes
4
replies
898
views
Handle zero effective gene length when tximport RSEM results
tximport
edgeR
updated 8 months ago by
Michael Love
42k • written 8 months ago by
hanc
• 0
0
votes
2
replies
320
views
Error in featureCounts matrix
GenomeWideAssociation
countsimQC
RNASeq
updated 10 weeks ago by
Gordon Smyth
50k • written 10 weeks ago by
ryann
• 0
11
votes
5
replies
7.4k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 22 days ago by
Garrett
• 0 • written 9.1 years ago by
brohawndg
▴ 150
2
votes
2
replies
198
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 21 days ago by
James W. MacDonald
65k • written 22 days ago by
sansan
• 0
1
vote
4
replies
253
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 18 days ago by
James W. MacDonald
65k • written 22 days ago by
Mirella Aurora
• 0
3
votes
3
replies
354
views
permutation test in edgeR
rna-seq
edgeR
updated 20 days ago by
Gordon Smyth
50k • written 4 weeks ago by
Netanel
• 0
4
votes
7
replies
883
views
weird volcano plot
DESeq2
updated 9 weeks ago by
Shuning
• 0 • written 6 months ago by
shouzheng
▴ 10
5
votes
6
replies
860
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
2
votes
7
replies
4.7k
views
Installing Local packages in Bioconductor
package
updated 8 months ago by
Boxun
• 0 • written 2.0 years ago by
BioC123
• 0
10
votes
10
replies
7.1k
views
biomaRt not working - lazy table error
error
lazy
R
biomaRt
table
updated 7 weeks ago by
juo5
• 0 • written 6 months ago by
Abhishek
▴ 10
6
votes
11
replies
1.0k
views
Packages don't update, but no error or warning is thrown
Bioconductor
3 months ago • updated 12 weeks ago
gernophil
• 0
0
votes
2
replies
293
views
RNAseq analysis
rnaseqGene
edgeR
DEGraph
DifferentialExpression
updated 8 weeks ago by
Gordon Smyth
50k • written 8 weeks ago by
z_bahari
• 0
1
vote
2
replies
1.2k
views
How to combine a bulk and pseudobulk dataset?
DESeq2
limma
RNASeq
RNASeqData
written 12 months ago by
informatician
• 0
0
votes
9
replies
2.5k
views
DESeq2 result really different when only use some sample vs all sample
deseq2
rnaseq
updated 6 months ago by
blowfish
• 0 • written 6.5 years ago by
bharata1803
▴ 60
3
votes
8
replies
920
views
DropletUtils read10xcounts adds the 12 Cell Multiplexing Oligo tags as gene names
DropletUtils
droplet
written 5 months ago by
pcantalupo
▴ 10
0
votes
3
replies
164
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 21 days ago by
James W. MacDonald
65k • written 21 days ago by
bas_work
▴ 30
2
votes
2
replies
320
views
locfunc not found in DESeq2
locfunc
DESeq2
shorth
estimateSizeFactors
11 weeks ago
Hope
▴ 10
7
votes
6
replies
4.2k
views
Conversion of UniProt to Ensembl
biomaRt
ensembldb
UniProt.ws
updated 7 months ago by
Marcel Ramos
690 • written 21 months ago by
Recep
▴ 20
0
votes
2
replies
1.3k
views
Error: BiocParallel errors
xcms
msdata
BiocParallel
8 months ago
mavamay
• 0
2
votes
5
replies
1.3k
views
removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2
BatchEffect
limma
updated 9 months ago by
Gordon Smyth
50k • written 9 months ago by
Sara
• 0
2
votes
3
replies
1.2k
views
Problem with function combine regarding merging two data frames based on their common rows
bioconductor
merge data frames
combine
biocgenerics
8.5 years ago • updated 6 months ago
Konstantinos Yeles
▴ 80
0
votes
2
replies
129
views
DESeq2 v1.35.0
DESeq2
updated 8 days ago by
Michael Love
42k • written 8 days ago by
Espresso
• 0
3
votes
3
replies
395
views
plotUMAP Gene Set Faceted
scater
updated 3 months ago by
alan.ocallaghan
▴ 160 • written 3 months ago by
Dario Strbenac
★ 1.5k
8
votes
7
replies
1.8k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 4 days ago by
Sara
• 0 • written 6.7 years ago by
Sylvain Foisy
▴ 80
28
votes
21
replies
49k
views
deseq2 filter the low counts
deseq2
lowcount
updated 3 months ago by
Xiao
• 0 • written 9.2 years ago by
aristotele_m
▴ 40
3
votes
4
replies
2.9k
views
Protein differential Expression analysis
differential expression
proteomics
updated 8 months ago by
ATpoint
★ 4.1k • written 6.3 years ago by
cardin.julie
• 0
2
votes
3
replies
1.2k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR
tximport
RNASeq
DESeq2
updated 4 months ago by
swbarnes2
★ 1.4k • written 5 months ago by
Bo
• 0
2
votes
7
replies
2.4k
views
Blood cell composition adjustment in methylation EPIC array: ChAMP
MethylationArray
methylationArrayAnalysis
ChAMP
updated 7 months ago by
dorota.komar
• 0 • written 3.4 years ago by
Ankit
▴ 20
8
votes
12
replies
2.6k
views
DESeq2 1.40.0 binary install issue on macOS x86 (Bioconductor 3.17)
DESeq2
updated 12 months ago by
Michael Love
42k • written 12 months ago by
Michael Steinbaugh
▴ 90
6
votes
12
replies
5.0k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 18 days ago
shepherl
3.9k
0
votes
2
replies
1.0k
views
error when using M-values in ChAMP
ChAMP
updated 6 weeks ago by
hortense96
• 0 • written 6.3 years ago by
a.mcneill
• 0
2
votes
3
replies
321
views
seqlevelsStyle() not working
ensembldb
genomei
GenomeInfoDb
3 months ago
Kai Hu
▴ 70
2
votes
5
replies
11k
views
Conversion from counts to FPKM
counts
fpkm
fpkm()
normalization
deseq2
updated 6 months ago by
Hamza
• 0 • written 5.4 years ago by
chiara.facciotto
• 0
1
vote
6
replies
755
views
Help creating BSgenome object for new canine and feline genomes?
BSgenome
updated 10 weeks ago by
James W. MacDonald
65k • written 3 months ago by
Kate
• 0
1,000 results • Page
2 of 20
Recent ...
Replies
Comment: deseq2 results
by
swbarnes2
★ 1.4k
Ask the people who made the libraires if there was anything unusual in the QC of the outlier sample. Try to figure out what biologically …
Comment: Can't post a question containing code?
by
NATASHA
• 0
did you find a solution? I´m having the same problem
Comment: error
by
NATASHA
• 0
Please ignore, i didnt copy all the scrip
Comment: Extremely small p-values using Limma for proteomic data
by
James W. MacDonald
65k
If you ever find yourself using the `@` function, you should reconsider what you are doing. There are vanishingly small instances when an e…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
42k
Here is some example code <https://gist.github.com/mikelove/cbbc84634b6854c865cb5eb08ad9b245>
Votes
A: AIC-like measure for DESeq2
Comment: Extremely small p-values using Limma for proteomic data
Comment: Log-cpm values from limma
Comment: Log-cpm values from limma
Comment: deseq2 results
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