Showing : DESEQ2 • reset
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abnormal deseq2 normalization
deseq2
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
5
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3
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1.6k
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DESeq2 with multiple treatments but no replicates
deseq2 rna-seq
updated 6.3 years ago by 43k • written 6.3 years ago by ▴ 20
1
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1
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2.4k
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DESeq2 test LRT or WALD
deseq2 LRT WALD
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
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2
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1.8k
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lfcShrink in DESeq2
deseq2 apeglm
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
1
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1
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1.8k
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Using RUVs with known batches
ruvseq deseq2
updated 6.3 years ago by 43k • written 6.3 years ago by ▴ 30
4
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4
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6.1k
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TMM Normalization: DESeqDataSet: some values in assay are negative
deseq2 deseq normalization
updated 6.3 years ago by ▴ 40 • written 6.3 years ago by • 0
2
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4
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1.0k
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understanding DEseq2 interactions before/after releveling the baseline
deseq2
updated 6.3 years ago by 43k • written 6.3 years ago by ▴ 140
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1
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1.3k
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Request for offset slot in DESeqDataSet objects
deseq2 EDASeq
updated 6.3 years ago by 43k • written 6.3 years ago by ▴ 100
1
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2
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970
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appropriate design formula
deseq2
updated 6.3 years ago by 43k • written 6.3 years ago by ▴ 10
2
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4
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1.1k
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Identifying cell line-independent DEG in a time series (DESeq2)
deseq2
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
0
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4
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2.8k
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DESeq2 pairwise comparison vs contrast function
deseq2
6.3 years ago dequattro.concetta ▴ 10
1
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2
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1.3k
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Filtering extraneous samples affects DESeq results. What is going on?
deseq deseq2
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
0
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3
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1.1k
views
could the result of DEseq2 by LRT be used in SPIA directly?
deseq2
updated 6.3 years ago by 43k • written 6.3 years ago by ▴ 10
5
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13
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9.5k
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DESeq2 for multiple groups
deseq2
updated 6.3 years ago by ★ 13k • written 6.3 years ago by ▴ 10
3
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5
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1.2k
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Multifactor design in DESeq2 - infection effect over time on three different plant cultivars
quinoa virus mutifactor design DESeq2
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
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4
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2.0k
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Extract residuals from DESeq2 fit
deseq2 residuals
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
0
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2
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5.4k
views
Heatmap of selected genes
heatmap DEGs RNAseq DESeq2
updated 6.3 years ago by ▴ 280 • written 6.3 years ago by • 0
1
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7
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2.8k
views
How to merge two tximport object into one dataset for DESeqDataSetFromTximport
deseq2 tximport
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
8
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8
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13k
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Steps needed to change design (relevel factors) in DESeq2
deseq2 DESeq2
updated 2.2 years ago by • 0 • written 6.3 years ago by ▴ 40
3
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3
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1.3k
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DESeq2: Sample outlier patterns 'switching' after normalization
deseq2 normalization
updated 6.3 years ago by 43k • written 6.3 years ago by ▴ 40
1
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4
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1.2k
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Interpretation of the heatmap produced by DESeq2
DESeq2
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
1
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2
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665
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too few replicates to observe statistically significant differences
deseq2
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
1
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3
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1.1k
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deseq2 formula design
deseq2
updated 6.3 years ago by ★ 1.4k • written 6.3 years ago by ▴ 10
1
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7
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1.9k
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Cannot generate a DEseq2DataSet from my data - DESeqDataSetFromMatrix returns error
deseq2 rlog
updated 6.3 years ago by 43k • written 6.3 years ago by ▴ 10
0
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7
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1.0k
views
DESeq2 analysis for low RNA input
deseq2
6.3 years ago capricygcapricyg ▴ 10
2
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3
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2.1k
views
RNAseq and heatmap
deseq2 RNA-seq Heatmap
updated 6.3 years ago by 43k • written 6.3 years ago by ▴ 10
1
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2
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1.3k
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Random effects in DESeq2
deseq2
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
0
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6
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1.5k
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DESeq2: Error when correcting batch effect
deseq2 batch effect
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
2
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5
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1.9k
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DESeq2-result files (.csv): Is there a convention for the IDs (e.g. gene names if produced for genes)
deseq2 gene format
6.3 years ago miriam.mueller • 0
3
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7
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1.5k
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Questions for ResultsNames() and the Contrast function
deseq2
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
8
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1
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11k
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What can I do if I only have TPM but not raw counts data?
deseq2
updated 6.3 years ago by ★ 13k • written 6.3 years ago by ▴ 30
5
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5
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6.2k
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tximport transcript missing
deseq2 salmon tximport
6.3 years ago mr6518849 ▴ 10
0
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4
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900
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DESeq2 nested effect with 5 variables
deseq2 RNA-seq
updated 6.3 years ago by 43k • written 6.3 years ago by ▴ 10
4
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4
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1.3k
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normalization of RNA-seq data after over-expressing the transcription factors
limma deseq2 voom edgeR
updated 6.3 years ago by ★ 29k • written 6.3 years ago by ▴ 670
0
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1
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808
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Incorrect DESeq2 Output
deseq2
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
0
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6
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1.4k
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DESeq2: Contrasts in multifactor design with interaction terms
r deseq2
6.3 years ago arielle • 0
0
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2
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1.4k
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Contrast vs relevel (DESEq2)
deseq2 RNAseq
updated 6.3 years ago by 43k • written 6.3 years ago by ▴ 10
0
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3
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2.9k
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DESeq2 more than 2 groups comparison
deseq2
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
2
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3
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1.2k
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collapseReplicates changes the order of the original dataframe in DESeq2
deseq2 collapseReplicates
updated 6.3 years ago by 43k • written 6.3 years ago by ▴ 10
0
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7
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6.1k
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DEseq2 ncol(countData) == nrow(colData) is not TRUE Error
deseq2
6.3 years ago trumbia • 0
0
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4
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3.6k
views
deseq2 correction batch effect without design
deseq2 batch effect
updated 6.3 years ago by ★ 1.4k • written 6.3 years ago by • 0
1
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1
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1.3k
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Deciphering Wilkinson Notation and Predictor Variables
deseq2
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
0
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4
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813
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DESeq2 "Not full rank" Error
deseq2
updated 6.3 years ago by ★ 1.4k • written 6.3 years ago by • 0
1
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8
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1.8k
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log2foldchange vs density plot from likelihood and posterior
deseq2
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
5
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11
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4.5k
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DESeq2 logfoldchange and interaction in model
deseq2 R logfoldchange rna-seq
6.5 years ago • updated 6.3 years ago pierre.marin • 0
0
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1
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1.0k
views
RNASeq biplot variables and samples
deseq2 rnaseq
updated 6.4 years ago by 43k • written 6.4 years ago by ▴ 30
0
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5
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2.6k
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RNA-seq time course analysis with only one experimental condition
deseq2 cancer rna-seq time-series
6.4 years ago mah19 • 0
1
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9
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2.6k
views
Comparing two different sequencing method by DEseq2
deseq2
updated 6.4 years ago by ★ 1.4k • written 6.4 years ago by • 0
1
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3
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2.7k
views
DESeq2: name and contrast arguments return partially different results under specific circumstances -- bug?
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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1.6k
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DESeq2 formula to include batch AND patient, and condition ?
deseq2
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
4,839 results • Page 48 of 97
Recent ...
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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