Showing : apeglm • reset
0
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1.0k
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Install old version of DESeq2
apeglm Install DESeq2 version
updated 16 days ago by ★ 4.0k • written 5 months ago by • 0
0
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1
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691
views
Which of apeglm and ashr may be more appropriate for pseudobulked DESeq2 analysis of single-cell RNA-seq data?
apeglm DESeq2
updated 3 months ago by 43k • written 3 months ago by • 0
0
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4
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880
views
Using shrunken LFC and s-value from DESeq2 as DGE results
apeglm s-value DESeq2
updated 4 months ago by 43k • written 4 months ago by • 0
3
votes
1
reply
649
views
DESeq2 Apeglm Coefficient Reordering / Log2FoldChange Comparison Change
DESeq2 apeglm
updated 6 months ago by 68k • written 6 months ago by • 0
1
vote
2
replies
690
views
Questions in Regards to LFC shrinkage in DESeq2
Dseq2 RNASeqData apeglm
15 months ago Gordon • 0
2
votes
10
replies
1.6k
views
How to run allelic imbalance in apeglm
apeglm
18 months ago euge.eugenio ▴ 20
0
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1
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1.6k
views
lfcShrink error: the line search routine failed
apeglm DESeq2
updated 21 months ago by 43k • written 21 months ago by • 0
0
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2
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2.0k
views
Error: insufficient numeric precision during Log fold change shrinkage with apeglm
apeglm
updated 2.3 years ago by 43k • written 2.3 years ago by • 0
0
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4
replies
1.4k
views
lfc direction of effect flipped for ashr, apeGLM, but accurate to biological data for non-shrunken
DESeq2 apeglm DESeq ApeGLM Ashr
updated 2.4 years ago by 43k • written 2.4 years ago by ▴ 20
2
votes
7
replies
3.0k
views
optimHess problem in apeglm/DESeq2
DESeq2 apeglm
updated 2.6 years ago by 43k • written 2.6 years ago by ★ 5.0k
3
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2
replies
1.5k
views
DESeq2 lfcShrink: swapping reference gives different results for the same comparison
DESeq2 apeglm
2.7 years ago Daphnia • 0
1
vote
5
replies
3.2k
views
DESeq2 outlier options and LFC Shrinkage
DESeq2 RNASeq RnaSeqSampleSize apeglm
updated 3.3 years ago by 43k • written 3.4 years ago by • 0
1
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3
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1.6k
views
LFC shrinkage setting negative LFC svalues to zero
DESeq2 DifferentialExpression apeglm
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
1
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2
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1.5k
views
running apeglm on a normal model and multiple coefficients
shrinkage apeglm
3.6 years ago Frederik Ziebell ▴ 30
1
vote
2
replies
1.8k
views
Use of shrunken LFCs to address questions about the distribution of LFCs between gene categories.
deseq2 apeglm DESeq2
3.9 years ago i.sudbery ▴ 40
2
votes
3
replies
2.7k
views
Choosing an svalue threshold from apeglm shrunken results in DESeq2
apeglm DESeq2
updated 4.2 years ago by 43k • written 4.3 years ago by ▴ 40
1
vote
5
replies
2.3k
views
lfcShrink probelm in many 0 count genes RNA-seq data
ashr DESeq2 apeglm
updated 4.3 years ago by 43k • written 4.3 years ago by ▴ 40
0
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1
reply
1.1k
views
Non-significant but high LFC after apeglm shrinkage
DESeq2 apeglm
updated 4.7 years ago by 43k • written 4.7 years ago by • 0
0
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1
reply
1.7k
views
Plotting the most expressed genes after conducting DESeq2
DESeq2 pheatmap apeglm
updated 4.8 years ago by 43k • written 4.8 years ago by ▴ 10
2
votes
2
replies
1.6k
views
DESeq2 in R
DESeq2 apeglm
updated 4.8 years ago by ★ 1.4k • written 4.8 years ago by ▴ 10
0
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2
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1.7k
views
DSEQ apeglm
DESeq2 apeglm
4.8 years ago amoaristotle ▴ 10
2
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1
reply
1.8k
views
apeglm -- influence of reference level on logFC and svalues
DESeq2 apeglm
updated 4.8 years ago by 43k • written 4.8 years ago by ★ 5.0k
0
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3
replies
1.5k
views
Using altHypothesis on apleglm-shrunken log2FoldChanges
apeglm DESeq2
4.9 years ago zefrieira • 0
0
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1
reply
1.5k
views
DESeq2 - shrunken LFC calculation
apeglm DESeq2
updated 4.9 years ago by 43k • written 4.9 years ago by ▴ 50
0
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3
replies
1.1k
views
Influence of DEG in ASE analysis within apeglm
apeglm
updated 5.2 years ago by 43k • written 5.2 years ago by • 0
1
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1
reply
1.0k
views
Exceeding Over-dispersion parameter bbEstDisp
apeglm bbEstdisp allele ratio
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
5
votes
10
replies
2.1k
views
Allelic imbalance in apeglm
apeglm Allelic imbalance concept
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
1
vote
4
replies
2.6k
views
Using different LFC shrinkage estimators for spike-in normalised RNA-seq data
deseq2 apeglm rna-seq spike-in
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 10
3
votes
2
replies
2.9k
views
lfcShrink function in DEseq2 and s-values
deseq2 apeglm
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 10
2
votes
1
reply
1.1k
views
What are the steps to use a complex model of Allelic imbalance through apeglm
apeglm complex model ASE Allelic imbalance
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
1
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1
reply
1.3k
views
Why s-values instead of p-values with non-default lfcThreshold and apeglm shrinkage in DESeq2
deseq2 apeglm
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
3
votes
4
replies
3.0k
views
Reporting S values? Reporting padj values?
deseq2 apeglm
updated 5.5 years ago by 43k • written 5.5 years ago by ▴ 20
4
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4
replies
4.0k
views
RNA seq analysis using Deseq2 and apeglm lfc shrinkage
deseq2 fdrtool apeglm
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
0
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2
replies
1.4k
views
Coefficient names for multiple group comparisons to use with lfcShrink & apeglm
deseq2 lfcShrink apeglm
updated 6.0 years ago by 43k • written 6.0 years ago by ▴ 20
0
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2
replies
1.8k
views
lfcShrink in DESeq2
deseq2 apeglm
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
3
votes
3
replies
2.1k
views
Using alternative LFC shrinkage methods for computing p-values in DESeq2
deseq2 apeglm statistics
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
3
votes
2
replies
2.2k
views
Calculate S/N ratios from apeglm for GSEA
apeglm fgsea Signal-To-Noise Ratio
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 20
2
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1
reply
1.4k
views
Deactivate svalue=T in lfcShrink - DESeq2 - apeglm
deseq2 apeglm
updated 6.7 years ago by 43k • written 6.7 years ago by ★ 5.0k
2
votes
4
replies
2.0k
views
What is the biological meaning of genes with FC = 0 after shrinkage
deseq2 apeglm
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
0
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2
replies
3.6k
views
DESeq2 coefficients for APEGLM-shrinkage
deseq2 apeglm
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
4
votes
4
replies
2.8k
views
Unexpected MAplot after apeglm shrinkage in DESeq2
apeglm deseq2 rna-seq
updated 7.1 years ago by 43k • written 7.1 years ago by ★ 5.0k
4
votes
2
replies
3.4k
views
Interpreting the results from lfcShrink() with apeglm in DESeq2
deseq2 apeglm lfcshrink
updated 7.2 years ago by 43k • written 7.2 years ago by ▴ 180
1
vote
4
replies
2.2k
views
Log2 fold-change shrinkage fails with lfcShrink when using the 'apeglm' method
deseq2 apeglm lfcshrink
7.4 years ago • updated 7.3 years ago coulsonr ▴ 20
0
votes
4
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1.8k
views
Error in Apeglm Method for Effect Size Shrinkage
deseq2 apeglm
updated 7.4 years ago by 43k • written 7.4 years ago by ▴ 50
10
votes
6
replies
7.6k
views
Log2FoldChange shrinkage method in DESeq2
deseq2 apeglm lfcshrink
updated 7.5 years ago by 43k • written 7.5 years ago by ▴ 90
45 results • Page 1 of 1
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Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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