Showing : DEseq2 • reset
2
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2.6k
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DESeq2 count outlier replacement from Cook's threshold
deseq2 deseq rnaseq outliers count outliers
updated 7.0 years ago by 43k • written 7.0 years ago by ▴ 10
0
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4
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1.3k
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DESeq2: Analyzing just two normal+tumour pairs
deseq2 reporting tools
7.0 years ago mmokrejs • 0
0
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2
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1.6k
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Get normalized COUNTS Deseq2
deseq2 normalized counts
updated 7.0 years ago by ★ 13k • written 7.0 years ago by • 0
0
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6
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2.4k
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large range of LFC in DESeq2
deseq2 lfc betaprior
updated 3.1 years ago by 43k • written 7.0 years ago by • 0
0
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3
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4.6k
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Data normalization and transformation using DESeq2
deseq2 normalization rnaseq rlog transformation variancestabilizingtransformation
7.0 years ago chiara.facciotto • 0
2
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2
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1.2k
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DESeq results gives all genes
deseq2 design matrix results
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
7
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7
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9.8k
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DESeq2 likelihood ratio test (LRT) design - 2 genotypes, 4 time points
deseq2 LRT rnaseq design reduced model
updated 7.0 years ago by • 0 • written 8.6 years ago by ▴ 50
1
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3
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939
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DeSeq2 with extremely variable samples
deseq2
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
0
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1
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1.6k
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DESeq2 PCA plotting
deseq2 michael love
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
0
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1
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1.2k
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DESeq2 then fdrtool
deseq2 fdrtool
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
0
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3
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1.4k
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collapseReplicates changes order of factors
deseq2 bug
7.0 years ago António Miguel de Jesus Domingues ▴ 510
1
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3
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6.0k
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DESeq2 estimateSizeFactors with control genes
deseq2 differential gene expression controls references
updated 8 months ago by • 0 • written 7.0 years ago by • 0
2
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4
replies
2.2k
views
Inconsistent result between limma/voom and DESeq2
deseq2 limma voom limma-voom rnaseq
updated 7.0 years ago by 53k • written 7.0 years ago by ▴ 60
12
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4
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5.2k
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WGCNA following salmon/DESeq2
deseq2 wgcna salmon
updated 7.0 years ago by ★ 3.0k • written 7.0 years ago by ▴ 30
2
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3
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2.7k
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GC content correction in salmon/deseq2 workflow for single-end RNAseq data
salmon edaseq rna-seq deseq2
updated 7.0 years ago by 43k • written 7.0 years ago by ▴ 30
0
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4
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2.6k
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DESeq2 for Cut&Run and differential enrichment testing
deseq2 Cut&Run
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
0
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2
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1.4k
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logfold shrinkage DESeq2
deseq2
7.0 years ago sherajilir • 0
0
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1
reply
1.9k
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DESeq2 paired design with missing samples and multiple conditions
deseq2 paired samples missing data multiple treatments
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
0
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2
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1.9k
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MA plot scattering pattern
deseq2 MAplot
7.0 years ago avitalwasser • 0
1
vote
1
reply
570
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Do I have too many samples or are some samples causing issues?
deseq2
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
6
votes
7
replies
2.7k
views
Normalization for small non-coding RNA
TMM deseq2 smallrna rnaseq
updated 7.0 years ago by ▴ 510 • written 7.0 years ago by ▴ 90
0
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1
reply
752
views
DESeq2 on mixed species samples
deseq2
updated 7.0 years ago by 68k • written 7.0 years ago by ★ 1.4k
1
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1
reply
3.8k
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Question regarding class imbalance and low sample size for DESeq2
deseq2
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
0
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4
replies
1.8k
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DESeq2 multifactor formula design
deseq2 time series multiple factor design
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
0
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2
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1.8k
views
DESeq2 Design with Multiple Replicates of Individuals including Tumour and Normal
DESeq2 design and contrast matrix
7.0 years ago bruce.moran ▴ 30
1
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2
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1.1k
views
DESeq2 - assessing expression of low count genes
deseq2 HERVs low counts prefiltering dispersion estimates
updated 7.0 years ago by 43k • written 7.0 years ago by ▴ 40
0
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2
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3.6k
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DESeq2 coefficients for APEGLM-shrinkage
deseq2 apeglm
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
0
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1
reply
965
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DESeq2 ratio of small p-values plot
deseq2 diagnostic plots
updated 7.0 years ago by 43k • written 7.0 years ago by ▴ 10
4
votes
9
replies
4.1k
views
DESeq2 - Upgrade from 1.20.0 to 1.22.1 now gives warnings 'package:stats' may not be available when loading
deseq2
updated 7.0 years ago by 25k • written 7.0 years ago by ▴ 30
0
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3
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1.3k
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Pairwise comparisons for "both between and within subject"experiment using DESeq2
pairwise deseq2 extracting contrasts resultsnames results deseq2
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
0
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3
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2.9k
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DESeq2: removal of duplicated genes during statistical analysis
deseq2 gene symbol ensembl
updated 7.0 years ago by 43k • written 7.0 years ago by ▴ 10
1
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1
reply
1.2k
views
DEseq2 with different fastq read numbers after salmon
deseq2 salmon rna seq salmon
updated 7.0 years ago by 43k • written 7.0 years ago by ▴ 10
0
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1
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2.7k
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converting mstrg labels from stringtie and prepDE.py to gene symbol for downstream biology
deseq2
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
4
votes
7
replies
1.9k
views
Are spurious correlations possible in correlating two DESeq2 foldchanges computed using the same reference sample group?
deseq2 correlation
7.0 years ago Cornwell, Adam ▴ 110
0
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1
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1.5k
views
DESeq2 - shrunken log fold changes and threshold test
deseq2 lfcshrink lfcthreshold differential gene expression
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
0
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4
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1.4k
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DESeq2 analysis design - different individuals for all samples
deseq2 rnaseq model.matrix experimental design
7.0 years ago Maithê Barros ▴ 10
0
votes
1
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761
views
Issue with normalization in DESeq2
deseq2 normalization rnaseq
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
0
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6
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1.6k
views
Another Matrix is not full rank question, multi-factor design issues
deseq2 model matrix not full rank multiple factor design
updated 7.0 years ago by 68k • written 7.0 years ago by • 0
0
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7
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1.8k
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Double nested design in DESeq2
deseq2
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
6
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8
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3.9k
views
alpha in lfcshrink?
deseq2
updated 4.6 years ago by ▴ 80 • written 7.0 years ago by ▴ 20
0
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1
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1.4k
views
How to keep the genes whose counts are equal or greater than 10
deseq2 filtering
updated 7.0 years ago by 68k • written 7.0 years ago by • 0
0
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3
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1.0k
views
Pre-filtering results influence on downstream analysis
deseq2 rnaseq
updated 7.0 years ago by 43k • written 7.0 years ago by ▴ 20
4
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8
replies
50k
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What is colData? How do I make one?
deseq2 coldata
updated 7.0 years ago by ★ 1.4k • written 7.0 years ago by ▴ 10
1
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1
reply
866
views
DESeq2 namespace load fail
deseq2
updated 7.0 years ago by ★ 13k • written 7.0 years ago by • 0
3
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3
replies
1.7k
views
How to decide whether a variate should be in the model or not
deseq2 rnaseq
updated 2.8 years ago by 43k • written 7.0 years ago by ▴ 20
0
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2
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1.1k
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Getting an error trying to do tximportData tutorial
deseq2 tximport
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
5
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8
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1.7k
views
High normalized counts on DESeq2 MAplot
deseq2 maplot
updated 7.0 years ago by 68k • written 7.0 years ago by ▴ 60
1
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4
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1.1k
views
importing Tximport to DESeq2 for a time series experiment
deseq2 tximport
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
0
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0
replies
660
views
Converting DESeq2 results to DiffBind object
deseq2 diffbind
7.0 years ago rbronste ▴ 60
1
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6
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1.2k
views
what is the correct command line to import my txi data file as a deseq2 dataset in a time series experiment
deseq2
7.0 years ago ahmedaalkarim • 0
4,840 results • Page 57 of 97
Recent ...
Replies
Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Comment: upstream git branches of bioc-release by Jeroen ▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
Votes
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
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Awards • All
Popular Question to shepherl 4.2k
Popular Question to Gordon Smyth 53k
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Popular Question to James W. MacDonald 68k
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