Showing : DEseq2 • reset
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DESeq2 for ChIP-seq
deseq2 diffbind
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
3
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7
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1.6k
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The discrepancy between the mean of extracted fitted value and calculated mean and SE based on LFC.
deseq2 deseq
7.3 years ago blastzone.heimerdinger ▴ 20
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4
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1.6k
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how do compare with DESeq2
deseq2
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
0
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8
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2.8k
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DESeq2 Multi factor, multi time point comparison design formula
rna-seq deseq2 deseq R
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
0
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1
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789
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Cultivar+Time+Treatment study in Deseq2
bioconductor deseq2
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
0
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8
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4.9k
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DESeq2: handling NA values in colData
deseq2 coldata NA
updated 15 months ago by 43k • written 7.3 years ago by ▴ 170
3
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1
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1.2k
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DESeq2: Handling batch effects with only one control replicate coming from another batch
deseq2 rna-seq
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
0
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1
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1.4k
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Invalid class DESeqDataSet object with Phyloseq
deseq2 phyloseq
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 10
7
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4
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1.9k
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DESeq2 error: "vector: cannot make a vector of mode 'S4'"
deseq2
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 20
1
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4
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2.2k
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Log2 fold-change shrinkage fails with lfcShrink when using the 'apeglm' method
deseq2 apeglm lfcshrink
7.3 years ago coulsonr ▴ 20
2
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6
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1.3k
views
accounting for technical variation in DESEQ2
deseq2 normalization
updated 7.3 years ago by ★ 3.0k • written 7.3 years ago by ▴ 10
1
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10
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2.9k
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Ribo-seq/RNA-seq analysis -- DESeq2 multi-factor design
deseq2 sequencing ribosome profiling riboseq multiple factor design
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 10
1
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9
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2.0k
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DESeq2 - v1.18 different p-values from v1.20 (Is it minmu?)
deseq2
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 20
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5
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7.9k
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DESEq2 - Change reference level change "Contrasts" results
deseq2
7.3 years ago andrebolerbarros ▴ 20
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3
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878
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A few up-regulated genes using an extravagant number of reads - effect on DE analysis
rnaseq deseq2
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
1
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7
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2.6k
views
skewed differentially expressed gene results - DESeq2
deseq2 differential gene expression outliers
updated 7.3 years ago by ★ 7.9k • written 7.3 years ago by ▴ 20
5
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9
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2.7k
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DESeq2 baseMean from DiffBind summarizedExperiment
deseq2 diffbind basemean summarizedexperiment
7.3 years ago rbronste ▴ 60
2
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4
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9.9k
views
Adding gene names (or symbols) in my DESeq result
rnaseq gene names deseq2
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 10
6
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4
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4.3k
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[DESeq2] Extracting results based on set thresholds
deseq2
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 10
0
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3
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2.1k
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Dose-response study with DESeq2 and no dose replicates
deseq2
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
0
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6
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1.0k
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DESeq2 / How to visualize differences into control conditions
deseq2
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
0
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1
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1.1k
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DESeq2 intstallation error on fedora
deseq2 R fedora qiime
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
0
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3
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1.9k
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RNA-seq data analysis with two species using DESeq2
DESeq2
updated 7.3 years ago by ★ 3.8k • written 7.3 years ago by ▴ 20
0
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3
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1.5k
views
time series RNA-seq allowing time offset between individuals
edgeR deseq2 rna-seq timecourse fittimeseries
updated 7.3 years ago by ★ 29k • written 7.3 years ago by • 0
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1
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2.0k
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Deseq2 default Cooks distance threshold
Deseq2 outliers cookscutoff
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
5
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4
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2.7k
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lfcShrink behavior with homogeneous expression dataset
deseq2 lfcshrink betaprior
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 110
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1
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1.6k
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DESeq2/tximport 'duplicate rownames not allowed' error
tximport deseq2
7.3 years ago ctl • 0
14
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5
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25k
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Dealing with genes that have Padj=NA
deseq2
updated 2.3 years ago by • 0 • written 10.0 years ago by ▴ 60
6
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4
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8.0k
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DESeq2 with proteomics data
deseq2
updated 7 months ago by • 0 • written 7.4 years ago by ▴ 10
2
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5
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5.4k
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Batch Effect Correction
batch effect removebatcheffect edgeR rld DEseq2
7.3 years ago Antonio Ahn ▴ 10
1
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3
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1.8k
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Help interpreting DESeq2 method for gene-wide dispersion estimates
deseq2 negative binomial model glm
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
0
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1
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741
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DESeq2 with too many rejections
deseq2
updated 7.3 years ago by 43k • written 7.4 years ago by ▴ 20
2
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4
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772
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Extract x and y values from plotDispEsts
R deseq2
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
2
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1
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2.9k
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Should I use alpine and can I convert the output back to counts?
alpine deseq2
updated 7.4 years ago by 43k • written 7.4 years ago by ▴ 20
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4
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2.5k
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DESeq2 I installed from latest Bionconductor version is still old version
deseq2 R bioconductor
updated 7.4 years ago by ★ 1.1k • written 7.4 years ago by • 0
3
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9
replies
3.4k
views
DESeq2 Normalized Counts for Mfuzz
deseq2 rnaseq mfuzz
updated 7.4 years ago by 43k • written 7.4 years ago by ▴ 50
0
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2
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874
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Times series - DE genes over the time of individual condition design matrix, LRT/Wald
deseq2
updated 7.4 years ago by 43k • written 7.4 years ago by ▴ 10
1
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2
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1.7k
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DESeq2 package for R 3.3.3
deseq2 R 3.3.3
7.4 years ago valentina.losardo • 0
3
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9
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2.6k
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deseq2 zeros in all treatments, fold change
deseq2
updated 7.4 years ago by 43k • written 7.4 years ago by ▴ 10
2
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2
replies
662
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Assessing within-individual and between-individual variability
deseq2
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
0
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3
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1.2k
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DESeq2 use of LRT
deseq2
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
3
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2
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1.2k
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Comparisons of comparisons in DESeq2
deseq2
updated 7.4 years ago by 43k • written 7.4 years ago by ▴ 10
1
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4
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1.4k
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Multiple comparisons with DESeq2
deseq2
updated 7.4 years ago by 43k • written 7.4 years ago by ▴ 10
0
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4
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916
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Advice on DESeq2 design
deseq2
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
0
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3
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1.5k
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time-series, no replicates, no control groupe
deseq2 time-series without replicate
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
0
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1
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2.3k
views
DeSeq2 installation on ubuntu fails
deseq2 R ubuntu bioconductor rstudio
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
0
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1
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509
views
Help with design for 2 controls in infection time points with deseq2
deseq2
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
3
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5
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1.1k
views
DESeq2: possible to compare read counts at single nucleotide level ?
deseq2 rnaseq
updated 7.4 years ago by 53k • written 7.4 years ago by • 0
1
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5
replies
2.2k
views
How do I stop DESeq2 from loading and additional errors related to the package.
r deseq2 error
updated 7.4 years ago by ★ 1.1k • written 7.4 years ago by • 0
0
votes
2
replies
3.3k
views
What are the different strategies to filter out low count genes?
rnaseq deseq2 differential gene expression
updated 7.4 years ago by ★ 13k • written 7.4 years ago by ▴ 80
4,840 results • Page 61 of 97
Recent ...
Replies
Comment: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
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.
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
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Popular Question to shepherl 4.2k
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Popular Question to James W. MacDonald 68k
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