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11
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2.0k
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globaltest question
Pathways
probe
affy
Pathways
probe
affy
written 17.7 years ago by
mike Ad.
▴ 30
2
votes
8
replies
532
views
Microarray Limma Model fitting and DEG
limma
DGEanalysis
updated 5 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
Amit
• 0
0
votes
26
replies
2.3k
views
How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges
nullranges
15 months ago • updated 40 minutes ago
Poonam
• 0
7
votes
36
replies
5.6k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 4 weeks ago by
Shiva
• 0 • written 5.5 years ago by
Guido Hooiveld
★ 3.9k
0
votes
17
replies
3.4k
views
What causes this DESeq2 error at "fitting model and testing"?
deseq2
differential expression
error
updated 10 months ago by
snow34
• 0 • written 6.6 years ago by
ap3637
• 0
1
vote
5
replies
2.1k
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
392
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
1.8k
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
1
vote
3
replies
895
views
Problem in running DESeq from expected count data of Transcriptome by Trinity followed by RSEM
Tissue
Spati
RSEM
deno
DEseq2
updated 10 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
3
votes
3
replies
13k
views
How to fix 'long vectors not supported yet' error in R
r
updated 4 weeks ago by
Amruta
• 0 • written 5.2 years ago by
r.tor
• 0
1
vote
3
replies
469
views
DESeq2: the model matrix is not full rank issue
DESeq2
updated 4 months ago by
malliardtee
• 0 • written 4 months ago by
Guangsheng
• 0
2
votes
3
replies
2.2k
views
Fail BiocManager::install(version='3.12')
BioManager
updated 7 weeks ago by
ATpoint
★ 4.1k • written 2.1 years ago by
liqidong52
▴ 20
3
votes
4
replies
8.6k
views
Gene-gene correlation analysis with RNA-seq
edgeR
updated 3 months ago by
Dimitris
• 0 • written 10.8 years ago by
Makis Motakis
▴ 30
0
votes
2
replies
229
views
WGCNA: analysis of complex trait associations with regressions
Regression
WGCNA
5 weeks ago • updated 4 weeks ago
w.cookson
• 0
0
votes
2
replies
557
views
Heat Map
ColData
pheatmap
DESeq2
written 10 months ago by
dania.khalid
• 0
4
votes
9
replies
1.3k
views
RNA seq differential expression analysis for large sample size
edgeR
DESeq2
9 months ago
Luca
• 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
828
views
Error: insufficient numeric precision during Log fold change shrinkage with apeglm
apeglm
updated 8 months ago by
Michael Love
41k • written 8 months ago by
Juan Pablo
• 0
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
2
votes
2
replies
183
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 15 days ago by
James W. MacDonald
65k • written 15 days ago by
sansan
• 0
9
votes
13
replies
6.5k
views
GSEA many significant gene sets despite no differentially expressed genes
GSEA
GeneSetEnrichment
DifferentialExpression
updated 12 weeks ago by
ATpoint
★ 4.1k • written 2.1 years ago by
nhaus
▴ 30
0
votes
6
replies
333
views
unable to access Annotationhub latest record
DNAMethylation
AnnotationHub
EPICv2manifest
annotation
updated 23 days ago by
Tim Peters
▴ 180 • written 4 weeks ago by
s.malik
• 0
0
votes
3
replies
4.2k
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 9 months ago by
fengjieli2021
• 0
4
votes
7
replies
865
views
weird volcano plot
DESeq2
updated 8 weeks ago by
Shuning
• 0 • written 5 months ago by
shouzheng
▴ 10
2
votes
2
replies
1.5k
views
Matching Variants Between Two VCF Objects
VariantAnnotation
written 3.4 years ago by
Dario Strbenac
★ 1.5k
9
votes
38
replies
6.8k
views
manipulate bedpe format files
GRanges
bedpe
structural variants
rtracklayer
written 8.2 years ago by
tangming2005
▴ 190
0
votes
2
replies
657
views
ChAMP - obtaining beta values using EPICv2 annotation
ChAMP
EPICv2
updated 3 months ago by
shuo
• 0 • written 3 months ago by
ChunkyJones
• 0
1
vote
7
replies
1.5k
views
enrichGOgradient color change
clusterProfiler
updated 6 weeks ago by
Guido Hooiveld
★ 3.9k • written 5 months ago by
inna.gur
• 0
0
votes
5
replies
705
views
Wondering how to look at the reads of a gene in samples to check if it was knocked out?
knockout
DESeq2
written 10 months ago by
Lillian
• 0
2
votes
6
replies
344
views
Factor vs Character in design
DESeq2
8 weeks ago
James Aiden
• 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 8 months ago by
Gordon Smyth
50k • written 8 months ago by
Sara
• 0
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
4
votes
7
replies
13k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq
R
edgeR
updated 7 months ago by
Gordon Smyth
50k • written 22 months ago by
Mohamed
▴ 30
3
votes
3
replies
368
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
6
replies
1.7k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 3 days ago by
Leonard Goldstein
▴ 200 • written 6.7 years ago by
Sylvain Foisy
▴ 80
6
votes
9
replies
763
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
28
votes
21
replies
48k
views
deseq2 filter the low counts
deseq2
lowcount
updated 3 months ago by
Xiao
• 0 • written 9.2 years ago by
aristotele_m
▴ 40
6
votes
11
replies
988
views
Packages don't update, but no error or warning is thrown
Bioconductor
3 months ago • updated 11 weeks ago
gernophil
• 0
0
votes
2
replies
1.4k
views
about baseMean in DEseq2
DESeq2
written 2.8 years ago by
Bogdan
▴ 670
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
2
replies
281
views
RNAseq analysis
rnaseqGene
edgeR
DEGraph
DifferentialExpression
updated 7 weeks ago by
Gordon Smyth
50k • written 7 weeks ago by
z_bahari
• 0
8
votes
12
replies
2.6k
views
DESeq2 1.40.0 binary install issue on macOS x86 (Bioconductor 3.17)
DESeq2
updated 11 months ago by
Michael Love
41k • written 12 months ago by
Michael Steinbaugh
▴ 90
0
votes
2
replies
837
views
DiffBind dropping peaks in ATAC-seq data
DiffBind
ATACSeq
updated 9 months ago by
Malcolm Cook
★ 1.6k • written 9 months ago by
Nebat
• 0
0
votes
2
replies
1.0k
views
error when using M-values in ChAMP
ChAMP
updated 5 weeks ago by
hortense96
• 0 • written 6.3 years ago by
a.mcneill
• 0
0
votes
2
replies
802
views
Recount3 data download problem
recount
recount3
updated 12 months ago by
Leonardo Collado Torres
★ 1.0k • written 17 months ago by
franceschini.gianmarco
• 0
0
votes
2
replies
618
views
Fluidigm Data Batch Correction
sva
limma
updated 9 months ago by
Gordon Smyth
50k • written 9 months ago by
Khushbu
• 0
0
votes
4
replies
1.9k
views
how to save subsetted GDS file
gwastools
written 6.0 years ago by
Adrienne Stilp
▴ 30
1,743 results • Page
2 of 35
Recent ...
Replies
Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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