Showing : DESEQ2 • reset
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File type for DEseq using ATACseq data
deseq2
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
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2
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1.8k
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DESeq2 error on analyzing microbiome data
deseq2 microbiome sequencing
6.4 years ago zhigang.li • 0
0
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1
reply
456
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Retrieving Normalized Groups from Results()
deseq2
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
0
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1
reply
578
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Should I subsample an over-clustered sample for DESeq2?
deseq2
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
5
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18
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2.7k
views
Difference of difference, paired design
edger deseq2 limma
updated 6.4 years ago by ★ 1.4k • written 6.4 years ago by • 0
0
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2
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678
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Creating the correct design
deseq2
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
2
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1
reply
886
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Using altHypothesis with shrunken LFC values in DESeq2
deseq2
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
1
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5
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2.6k
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Paired samples in cell lines using DESeq2
deseq2
updated 6.4 years ago by 43k • written 6.4 years ago by ▴ 10
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3
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1.4k
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Analysis strategy - possible to use naive control group as t=0 for two treatment groups?
Deseq2 design time course basal group
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
27
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17
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9.9k
views
DESeq2 1.20.0 lfcshrink function
deseq2 differential expression logfoldchange lfcshrink lfcthreshold
updated 4.5 years ago by 43k • written 7.4 years ago by ▴ 50
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6
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2.4k
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deseq2 pre filter rna seq
deseq2 rnaseq
updated 2.1 years ago by 43k • written 6.4 years ago by • 0
0
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0
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1.4k
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Including sva results in SeqGSEA with data with batch effect
limma deseq2 seqgsea sva deseq
6.4 years ago kentfung ▴ 20
1
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4
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1.6k
views
Creating contrasts which do not include the reference level in limma, edgeR or DESeq2
limma deseq2 edgeR
updated 6.4 years ago by 68k • written 6.4 years ago by ▴ 50
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2
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4.1k
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Anbiguous instruction on how to set the blind value in DESeq2's vst function
deseq2
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
2
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4
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924
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Error in summary.DESeqResults(res) : could not find function "summary.DESeqResults"
deseq2 DEseq2
updated 6.4 years ago by 43k • written 6.4 years ago by ▴ 30
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3
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1.0k
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More Info on results names
deseq2
6.4 years ago dennism9251 • 0
0
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5
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1.5k
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Question regarding model matrix in limma.
limma deseq2
updated 6.4 years ago by 68k • written 6.4 years ago by ▴ 50
0
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1
reply
777
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Get gene level summaries from table of transcript level quantification
tximport deseq2
updated 6.4 years ago by 68k • written 6.4 years ago by • 0
1
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2
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1.0k
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Batch correction for two conditions two batches
deseq2
updated 6.4 years ago by ★ 1.4k • written 6.4 years ago by • 0
4
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18
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27k
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DEseq2 time-series design.
deseq2 timecourse design
updated 6.4 years ago by • 0 • written 11.0 years ago by ▴ 100
1
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9
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5.2k
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Difference between log2FC(MLE) and calculated log2 fold change in DESeq2 ver 1.20.0
deseq2
updated 4.5 years ago by • 0 • written 6.4 years ago by • 0
0
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9
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1.7k
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Deseq issues - pipeline all of a sudden stopped working
deseq2
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
1
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3
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960
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estimateSizeFactors after subsetting?
deseq2
updated 6.4 years ago by 43k • written 6.4 years ago by ▴ 20
0
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3
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870
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FNR in RNASeq
deseq2 edger
updated 6.4 years ago by 53k • written 6.4 years ago by • 0
0
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4
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2.4k
views
DESeq2 compare all_vs_all levels error
deseq2 error RNAseq
updated 6.4 years ago by ★ 1.4k • written 6.4 years ago by ▴ 30
1
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3
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1.9k
views
Combining multiple L2FC values and determining variance
deseq2
6.4 years ago David Eccles (gringer) ▴ 30
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1
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1.3k
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[DESeq2] LFC shrinkage and p-adjusted output
deseq2 normalization
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
0
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1
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1.2k
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DESeq2: three conditions lfcShrink CvsB analysis
deseq2 lfcShrink
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
1
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7
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1.4k
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how to set design for this DOE in DESeq2
deseq2
updated 6.4 years ago by 43k • written 6.4 years ago by ▴ 10
0
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1
reply
787
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Help with formula design for DESeq2
DESeq2
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
3
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4
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3.0k
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MDS plotting within the limma/voom workflow
limma voom deseq2
updated 6.4 years ago by 53k • written 6.4 years ago by ▴ 50
0
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7
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3.8k
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Issue installing RNA-seq workflow
software error deseq2 workflow rnaseqGene
updated 6.4 years ago by 25k • written 6.4 years ago by • 0
0
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1
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427
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DESeqDataSetFromMatrix error: dds file described as <Object with null pointers>
deseq2
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
1
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8
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3.5k
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DESeq2/SummarizedExperiment RStudio shows Object With Null Pointer
deseq2 null summarizedexperiment rstudio
updated 6.4 years ago by 25k • written 6.4 years ago by • 0
9
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10
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3.0k
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Any efficient workaround to identify highly variable genes in Affymetrix microarray expression data?
limma microarray genefilter deseq2
6.4 years ago Jurat Shahidin ▴ 80
0
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1
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903
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DESeq2 analysis of multifactorial RNAseq experiment
deseq2 design time-course
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
2
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2
replies
1.4k
views
DESeq2 outlier flagging with 2 replicates
deseq2
updated 6.4 years ago by 43k • written 6.4 years ago by ▴ 10
0
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1
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579
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Question: DESeqDataSetFromMatrix error: dds file described as <Object with null pointers>
deseq2
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
10
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4
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19k
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Removing batch effect with limma::removeBatchEffect() actually exacerbates the effect
limma deseq2
updated 6.4 years ago by 53k • written 6.4 years ago by ▴ 30
1
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1
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805
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Error in function classes fdef mtable unable to find an inherited method for function assay for signature function missing
deseq2
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
0
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2
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1.1k
views
DESeqDataSetFromTximport gives <Object with null pointer>
deseq2 software error
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
0
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1
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1.0k
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[DESeq2] sequin [ANAQUIN] correction, too many factors in model
deseq2 ruvseq anaquin sequins
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
2
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5
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856
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[DeSeq2] Developmental timeline across seasons with non-independent sampling
deseq2
6.4 years ago João Pimenta • 0
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4
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1.5k
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DESeq2 log fold change
deseq2
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
1
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1
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1.4k
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All Pairwise Comparisons with DESeq2 While Controlling for Batch Effects: Does Reference Level Matter?
deseq2 differential expression batch correction design
updated 6.4 years ago by 43k • written 6.4 years ago by ▴ 40
0
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2
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2.0k
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DESeq2 Interaction Term Interpretation for Microbiome Data
deseq2 microbiome
updated 6.4 years ago by ★ 1.4k • written 6.4 years ago by • 0
0
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1
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1.4k
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DESeq2 analysis with high within-group variability across several groups
DESeq2
updated 6.4 years ago by 43k • written 6.4 years ago by ▴ 20
2
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6
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2.0k
views
How to add row data to DESeqDataSetFromMatrix
deseq2
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
1
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1
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702
views
How can I import data generated from different sources (salmon and gene count matrix) to generate DESeqDataSet object?
deseq2
updated 6.4 years ago by 43k • written 6.4 years ago by ▴ 30
1
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2
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791
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Too many DEGs
deseq2
updated 6.4 years ago by 43k • written 6.4 years ago by ▴ 20
4,839 results • Page 49 of 97
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Replies
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much, @ATpoint and @kevin , for your valuable insights. I have carefully checked all your suggestions. First, I examined th…
Answer: Finding duplicated entries in GRangesList by Kevin Blighe ★ 4.0k
The duplicated and unique functions operate element-wise on GRangesList objects. This means that they apply the respective function to each…
Answer: DESeq2 on non-RNASeq counts data by Kevin Blighe ★ 4.0k
The use of DESeq2 for count data from artificial sequences is acceptable, as the program models counts via a negative binomial distribution…
Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hello Rui Tang, The buffer overflow error in featureCounts that you encountered is likely due to a compatibility issue between the Subre…
Answer: Problem with the TMB plot by Kevin Blighe ★ 4.0k
The issue that you describe with the tumor mutational burden (TMB) plots appearing linear and lacking consistent TMB values across samples …
Votes
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Identifying differentially expressed genes in individual samples from a large co
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