Showing : DESEq2 • reset
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How to use DESeqDataSetFromHTSeqCount
deseq2
updated 5.6 years ago by ★ 1.4k • written 5.6 years ago by ▴ 20
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11
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3.0k
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DESeq2 generating different DEGs based on the order of samples listed in the colData = samples file
DESeq2
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
3
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1
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656
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Reverse calculate counts using DESeq2 normalised values
deseq2 rnaseq
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
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1
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822
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DESeq2 - why genes with very large variance between reps show up as significantly changed?
deseq2
5.6 years ago ninova • 0
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3
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925
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DESeq2 library problem
R deseq2
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
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1
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2.7k
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Using DeSeq2 on microRNA data
deseq2 mirdeep2 microRNA differential expression analysis
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
1
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3
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1.1k
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DESeq2 / agricolae packages conflict
deseq2 dependendies conflict agricolae
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
2
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2
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523
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rlog transformation for downstream analyses in DESeq2: Importance of experiment design
deseq2
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
3
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6
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2.0k
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Error:could not find function "DESeqDataSetFromHTSeqCount"
deseq2
updated 5.6 years ago by 25k • written 5.6 years ago by ▴ 30
1
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1
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388
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DESeq2 and adj p-value
deseq2
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
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5
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2.8k
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DESeq2: Comparing one sample with the mean of all
deseq2
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
0
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2
replies
594
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EdgeR-Timeseries w nested design
deseq2 edger
updated 5.6 years ago by 53k • written 5.6 years ago by • 0
0
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1
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1.7k
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Is LFC shrinkage necessary for all data?
deseq2 software error
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
2
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2
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852
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DESeq2 for ChIP/CLIP-seq: one-sided test
deseq2 diffbind
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
2
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2
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1.4k
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Mocking data for understanding interactions in DESeq2
deseq2 deseq
updated 5.7 years ago by ★ 3.8k • written 5.7 years ago by • 0
1
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4
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4.3k
views
Factor levels and Differential Expression analysis: Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) : contrasts can be applied onl…
deseq2
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
0
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1
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452
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DESeq2 for analyzing cell fractionation sequencing data
deseq2
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
1
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1
reply
601
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DESeq2 and large global transcription shut-down
deseq2
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
0
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5
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1.9k
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problem with DESeq2
deseq2
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
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1
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1.4k
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Removing low sequences before analysis
deseq2 normalization
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
0
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9
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1.9k
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Plotting change over time
deseq2 Plot
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
3
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5
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3.1k
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How to analyze pre-processed RNA-Seq data from GEO based on the deseq R package for filtering and DE analysis
deseq rna-seq filtering DE deseq2
updated 5.7 years ago by 43k • written 5.7 years ago by ▴ 840
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6
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4.3k
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Which of these (raw count, scaled estimate, normalized_results ) data of TCGA is best for finding the DEG (differentially expressed) genes by DESeq2 …
deseq2
5.7 years ago roohallah1435 • 0
4
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4
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4.0k
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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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1
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641
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Should rows with zero sum be excluded before calling the DEseq() function
deseq2
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
0
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3
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1.6k
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Nested design- phyloseq_to_deseq
deseq2 Phyloseq Nested
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
0
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3
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671
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Big difference between two-factor comparison when 3 factors data or when 2 factor data are used?
deseq2
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
0
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2
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1.2k
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DESEQ2: Error in checkFullRank(modelMatrix)
deseq2 miRNASeq designmatrix Batch
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
0
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1
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593
views
DESeq2 - groups with no replicates
deseq2
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
1
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2
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2.9k
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selecting result from deseq2
DESeq2
updated 11 weeks ago by 43k • written 5.7 years ago by • 0
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1
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834
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What happens when estimateSizeFactors() is added to the standard workflow before DESeq()?
deseq2
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
0
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1
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1.0k
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using deseq2 for intronic counts for 2 conditins with replicates
deseq2 intron differential expression
updated 5.7 years ago by 43k • written 5.7 years ago by ▴ 40
0
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4
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975
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.csv files from miRDeep2 to upload in R studio for DESeq2
deseq2
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
0
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2
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1.3k
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Limits of log2fold change (30, -30) with DESeq2 results
deseq2
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
0
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2
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627
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Count outliers differs per design will running DESeq
deseq2
updated 5.7 years ago by 43k • written 5.7 years ago by ▴ 30
0
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8
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6.3k
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Combining 2 datasets from 2 different RNAseq experiments
deseq2 normalization probe
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
1
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1
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23k
views
Why does the DESEQ2 lfcshrink function results not include the stat variable
deseq2 stat lfcshrink
5.7 years ago divercory • 0
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3
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763
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DEseq2 design tutorial with multiple experimental factors
deseq2 annotation normalization
5.7 years ago christophe.vanhaver • 0
1
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2
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2.9k
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Gene Clustering DESeq2 for results
deseq2
updated 5.7 years ago by 43k • written 5.7 years ago by ▴ 60
2
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1
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1.8k
views
Using DESeq2 for normalization of dataset with no replicates
normalization deseq2
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
0
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1
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1.9k
views
mcols(object)$betaConv. Use larger maxit argument with nbinomWaldTest")
deseq2
updated 5.7 years ago by 43k • written 5.7 years ago by ▴ 40
2
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4
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6.5k
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tximport, Kallisto and Deseq2 (quick answer)
kallisto tximport deseq2 counts
6.6 years ago • updated 5.7 years ago Mozart ▴ 30
1
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2
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789
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BATCH EFFECT OF AGE
deseq2
updated 5.7 years ago by 43k • written 5.7 years ago by ▴ 60
5
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10
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2.3k
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tximport and stevia, how to build tx2gene without any reference genome
deseq2 annotation
updated 5.7 years ago by 43k • written 5.7 years ago by ▴ 60
2
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4
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1.8k
views
DESeq2 result extraction
deseq2
updated 5.7 years ago by 43k • written 5.7 years ago by ▴ 40
1
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1
reply
911
views
DESeq2 paired test (for most samples)
deseq2 paired tumor vs normal
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
1
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9
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2.0k
views
Wrong results of DESeq compared to DESeq2 for some test cases?
deseq2 DESeq
updated 5.7 years ago by ★ 3.8k • written 5.7 years ago by • 0
0
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6
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912
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Why so few genes are returned?
deseq2
updated 5.7 years ago by ★ 4.0k • written 5.7 years ago by • 0
4
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2
replies
6.4k
views
DESeq2 Multiple Conditions: Do I need a "reference"?
deseq2
updated 5.7 years ago by ★ 4.0k • written 5.7 years ago by ▴ 10
1
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3
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1.5k
views
Design DESeq2 with one or more continues variables
deseq2
5.7 years ago adR ▴ 40
4,840 results • Page 41 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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