2
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2
replies
1.7k
views
DESeq2 results - Annotating and exporting results
DESeq2
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
3
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7
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1.7k
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DESeq2 alternative hypyothesis: testing for genes NOT significantly downregulated
DESeq2
2.4 years ago casco ▴ 10
2
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7
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5.5k
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EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 2.4 years ago by • 0 • written 4.7 years ago by ▴ 20
1
vote
2
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1.3k
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DiffBind plot.profile y-axis unit and individual locus value on the heatmap
DiffBind
2.4 years ago Junsik • 0
1
vote
0
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1.2k
views
Job: EMBL-EBI Data resources: Functional Genomics and Single Cell Biology Team Leader
JobPosting
2.4 years ago Wolfgang Huber ★ 13k
1
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4
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1.0k
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BioNero - problem with module_trait_cor function
BioNERO
2.4 years ago matevz.likar • 0
0
votes
1
reply
1.1k
views
SVA for MatrixeQTL - which "variable of interest"?
matrixeqtl sva
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
0
votes
9
replies
1.8k
views
DESeq2: How to estimate effects of one factor controlling for other factors?
DESeq2
2.4 years ago mjd275 • 0
1
vote
8
replies
4.3k
views
Significantly regulated genes produced by only a few affected samples
deseq2
written 7.9 years ago by ▴ 60
0
votes
9
replies
2.0k
views
How long does it usually take to complete dream() from start to finish?
variancePartition mixedmodel dream
2.4 years ago hayleyw • 0
3
votes
4
replies
4.1k
views
Protein differential Expression analysis
differential expression proteomics
updated 2.4 years ago by ★ 5.0k • written 8.0 years ago by • 0
2
votes
14
replies
2.7k
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ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno ChIPSeq
updated 2.4 years ago by 68k • written 2.4 years ago by ▴ 10
2
votes
12
replies
3.0k
views
P-value inflation?
DESeq2
updated 2.4 years ago by 68k • written 2.4 years ago by ▴ 10
1
vote
3
replies
1.4k
views
Merging Methylation data (M-values) with phenotypic data
MethylationArrayData methylationArrayAnalysis
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
0
votes
2
replies
940
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DiffBind error
DiffBind
updated 2.4 years ago by ★ 5.2k • written 2.4 years ago by • 0
0
votes
0
replies
860
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Getting CDS 5'/CDS3' incomplete flags info from ENSEMBL using biomaRt
biomaRt
2.4 years ago ali.oghabian • 0
1
vote
2
replies
1.5k
views
DESeq2 batch design
DESeq2
updated 2.4 years ago by ★ 1.4k • written 2.4 years ago by ▴ 10
2
votes
2
replies
1.0k
views
Broken UNITE 9.0 link (General FASTA Release)
dada2 UNITE
2.4 years ago GlycineMax • 0
1
vote
4
replies
1.3k
views
running Bioconductor Docker images only works with versions <= 3.15
Bioconductor
2.4 years ago patrick.turko • 0
0
votes
1
reply
877
views
TOMsimilarityFromExpr the returned matrix has NaN values except for diagonal 1
TOMsimilarityFromExpr WGCNA
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
0
votes
1
reply
878
views
Package "Netboost" is an Unix-only package, how can I install it in R?
Bioconductor netboost
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
0
votes
0
replies
936
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Try to understand better how to set out an effective sample size within the MetagenomSeq package in microbiome ?
Metagenomics metagenomeSeq microbiome phyloseq microbiomeDataSets
2.4 years ago Mohamed ▴ 30
0
votes
8
replies
3.7k
views
Question about filterByExpr function edgeR
edgeR
2.4 years ago lucap • 0
0
votes
1
reply
1.1k
views
Getting NAs in both p-values (normal and adjusted) in DEseq2
DESeq2
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
0
votes
1
reply
908
views
Cant post a bug report
msa
updated 24 months ago by ▴ 50 • written 2.4 years ago by • 0
0
votes
3
replies
1.2k
views
Is it possible to extract the expression of a single group without making comparisons?
MicroarrayData hta20transcriptcluster.db
updated 2.4 years ago by 53k • written 2.4 years ago by • 0
0
votes
2
replies
918
views
How to incorporate covariate factors into design to analyse a continuous variable?
DifferentialMethylation limma
written 2.4 years ago by • 0
8
votes
15
replies
3.4k
views
PCA percent variance DESeq2
PCA DESeq2
2.4 years ago IUH • 0
1
vote
6
replies
3.7k
views
Time-series RNA-seq analysis using DESeq2
time-series DESeq2 RNASeq timecoursedata TimeCourse
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
0
votes
7
replies
2.9k
views
error with champ.load
ChAMP champ methylation
updated 2.4 years ago by • 0 • written 5.8 years ago by • 0
0
votes
1
reply
1.1k
views
Why was the number of DEG different between DESeq results and count by myself using excel?
RNASeqData DEGseq
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
1
vote
3
replies
1.5k
views
Can CAMERA analyze just one particular pathway
pathway ORA limma CAMERA DGE
updated 2.4 years ago by 53k • written 2.4 years ago by • 0
0
votes
2
replies
917
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SPIAT for HALO manual phenotype entry
PHENOTYPE SPIAT HALO
updated 2.4 years ago by • 0 • written 2.6 years ago by • 0
0
votes
1
reply
978
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Comparing the effect of single drug and two-drug combination with control in RNA seq data
GeneExpressionWorkflow DESeq2
updated 2.4 years ago by 43k • written 2.4 years ago by • 0
0
votes
1
reply
660
views
DEG by deseq2 by Race
DESeq2
updated 2.4 years ago by ★ 4.0k • written 2.4 years ago by • 0
4
votes
9
replies
3.8k
views
DittoDimPlot errror: Cannot find 'NA' in this Seurat object
dittoSeq
updated 2.4 years ago by ▴ 10 • written 2.4 years ago by ▴ 10
5
votes
5
replies
1.6k
views
limma output for epic array methylation data
linearregression epicarray MethylationArray limma
2.4 years ago Jitendra ▴ 10
0
votes
1
reply
767
views
the confuse issue in DEseq2 among multi group
DESeq2
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
1
vote
4
replies
1.3k
views
Help for SeqVarData function
Biobase SeqVarTools
2.4 years ago pjuge • 0
1
vote
5
replies
1.2k
views
Errors with makeTxDbFromBiomart
biomaRt
updated 2.4 years ago by 68k • written 2.4 years ago by ▴ 10
1
vote
2
replies
1.6k
views
unable to retrieve certain packages from bioconductor 3.15
Bioconductor biocondu
updated 2.4 years ago by 68k • written 2.4 years ago by ▴ 10
2
votes
3
replies
1.6k
views
Rsubread: subjunc() loads index repeatedly
Rsubread
2.5 years ago • updated 2.4 years ago Gerhard Thallinger ▴ 180
0
votes
1
reply
708
views
Rbowtie2 on windows
Rbowtie2
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
3
votes
2
replies
3.1k
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG DESeq2 biomaRt clusterProfiler org.Mm.eg.db
updated 2.4 years ago by ★ 4.1k • written 2.4 years ago by ▴ 10
5
votes
2
replies
1.9k
views
can't install DESeq2 ("unable to access index for repository")
biocmanager DESeq2
2.4 years ago Alessia ▴ 40
6
votes
11
replies
3.6k
views
can't open mghp.osn.xsede.org
GenomeInfoDbData genomeinfodbdata
updated 20 months ago by ▴ 150 • written 2.4 years ago by ▴ 80
3
votes
2
replies
915
views
cant' download fgsea_1.20.0.tar.gz
download fgsea
2.4 years ago luca.s ▴ 50
8
votes
9
replies
2.2k
views
All three of the sites where genomeinfodbdata R packages are stored appear to be down.
GenomeInfoDbData
2.4 years ago 15753563659 ▴ 80
0
votes
3
replies
1.8k
views
Error with makeTxDbFromBiomart
DEXSeq biomaRt
updated 2.4 years ago by 16k • written 2.5 years ago by • 0
0
votes
1
reply
866
views
con vs treated group miRNA comparison using limma
mirTarRnaSeq miRNAData
updated 2.4 years ago by 53k • written 2.4 years ago by • 0
46,725 results • Page 45 of 935
Recent ...
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Answer: When to use edgeR or limma by Gordon Smyth 53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
I updated the above answer today.
Answer: When to use edgeR or limma by James W. MacDonald 68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Answer: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
The short answer is that limpa reads standard feature-level intensities from Spectronaut or other quantifications tools. limpa is designed …
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@gordonsmyth Noted, thank you very much.
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Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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