Showing : DESEQ2 • reset
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Differentially expression analysis of orthologous genes between two species
DESeq2 tximport
3.0 years ago Konstantinos • 0
0
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2
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804
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Setting up contrasts within a dataset within conditions (across different genotype) and across conditions (for the same genotype)
DESeq2
3.0 years ago nrama • 0
2
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3
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2.2k
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Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
3.0 years ago mohammedtoufiq91 ▴ 10
2
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1
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1.3k
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How to interpret DESeq2's padj after setting lfcThreshold and the log2FC is greater than lfcThreshold?
DESeq2
updated 3.0 years ago by 43k • written 3.0 years ago by ▴ 10
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2
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1.5k
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Deseq2 and co-expression network normalization
DESeq2 Normalization DifferentialExpression r
updated 3.0 years ago by ★ 5.0k • written 3.0 years ago by • 0
0
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1
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736
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DESeq2, normalization for within-sample comparison, and 3'-end RNAseq data
DESeq2
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
4
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2
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2.2k
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DESeq2 false positive result?
DESeq2
updated 3.0 years ago by ★ 1.4k • written 3.0 years ago by ▴ 10
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2
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1.4k
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Changing the sample order in the PCA plot
DESeq2
3.0 years ago turtle888 • 0
0
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2
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1.5k
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Remove low-expressed genes in DESeq2?
DESeq2 lowcountgenes deseq2 independent
written 3.0 years ago by • 0
2
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4
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5.8k
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Possibility of using TPM or FPKM values in edgeR for differential expression analysis?
DESeq2 R edgeR Normalization RNASeq
3.0 years ago mohammedtoufiq91 ▴ 10
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1
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750
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NA value in padj but only for certain contrasts
DESeq2
updated 3.0 years ago by 43k • written 3.0 years ago by ▴ 10
1
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12
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3.7k
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normalization of ChIP-seq data by using the spike-ins or by using total library sizes
DESeq2 edgeR limma
updated 3.0 years ago by 43k • written 3.0 years ago by ▴ 670
0
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1
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741
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DESeq2 : Using contrast in results vs performing complete independent analysis
DESeq2
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
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2
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1.4k
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Is it correct to plot Log2FC vs adj p-value from Likelihood ratio test?
DESeq2 adjp Volcano LRT
written 3.0 years ago by ▴ 10
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1
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1.2k
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Interpretation of coefficient when using "~ grp + grp:ind.n + grp:cnd"
DESeq2 interaction coefficient LinearModel RNASeq
updated 3.0 years ago by 43k • written 3.0 years ago by ▴ 10
0
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1
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889
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Design structure
DESeq2 des
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
1
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2
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1.2k
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Question about contrasts in DESeq2
DESeq2
3.0 years ago • updated 2.9 years ago marinaw ▴ 20
0
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1
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1.1k
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Interpreting results from DESeq2 time-series multifactorial data analysis
DESeq2 time-series timecoursedata timecourse multifactorial
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
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1
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857
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Strange dispersion plot with high outliers
DESeq2
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
0
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1
reply
963
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How to extract DeSeq2 results for the different groups?
DESeq2
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
0
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1
reply
842
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DESeq2 paired multifactor test
DESeq2 StatisticalMethod
updated 3.0 years ago by 43k • written 3.0 years ago by ▴ 10
1
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3
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1.7k
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Problem with DESeq2
DESeq2 apple-m1
updated 3.0 years ago by 43k • written 3.0 years ago by ▴ 10
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4
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1.5k
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Higher Dimensional RNASeq Clustering Significance
DESeq2 RNASeq PrincipalComponent pcaExplorer
written 3.0 years ago by • 0
0
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1
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1.7k
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DESeq2 design function and downstream analyses
DESeq2
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
0
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2
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1.3k
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Filtering normalised counts
DESeq2
updated 3.0 years ago by 68k • written 3.0 years ago by • 0
0
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1
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524
views
DESeq2 effect of interaction when using a grouping variable
DESeq2
updated 3.0 years ago by ★ 1.4k • written 3.0 years ago by • 0
1
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4
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1.1k
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DESeq2 says my sampleinfo has linear combination error but I don't see it...
DESeq2
updated 3.0 years ago by ▴ 780 • written 3.0 years ago by • 0
1
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2
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1.4k
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How to process and analyze Total RNA-Seq data?
DESeq2 R edgeR Normalization RNASeq
3.0 years ago mohammedtoufiq91 ▴ 10
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1
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1.3k
views
Error in DESeqDataSetFromHTSeqCount
DESeq2 RNA-seq HTseq DESeqDataSetFromHTSeqCount
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
0
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2
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1.5k
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ChIP-Seq Analysis: Comparing Unannotated Peaks with DESeq2
DESeq2 MACS2
3.0 years ago vanbelj ▴ 30
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5
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4.8k
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Error with DESeq2: DESeqDataSet(se, design = design, ignoreRank) : counts matrix should be numeric, currently it has mode: character
DESeq2
updated 3.0 years ago by ★ 5.0k • written 3.0 years ago by • 0
0
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1
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817
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Failed Construction of DESEQDataSet Object: C.Elegans
Celegans DESeq2 dds Errorinseq_len(length(idx)-1)
updated 3.0 years ago by 68k • written 3.0 years ago by • 0
0
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2
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1.4k
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DESeq2 correction for biological replicate variance using design
DESeq2
3.0 years ago lukas.krauss • 0
5
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18
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9.5k
views
Install DESeq2 problem for macbook pro M1 Max
Bioconductor Install DESeq2
updated 23 months ago by • 0 • written 3.8 years ago by • 0
0
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1
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1.1k
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Downstream analysis with Differentially Expressed Genes
DESeq2 GO goseq FunctionalAnnotation
updated 3.0 years ago by ▴ 10 • written 3.0 years ago by • 0
1
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3
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2.1k
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Interpretation of LRT results
DESeq2 LRT Heatmap
updated 2.1 years ago by 68k • written 3.0 years ago by ▴ 10
0
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2
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975
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Include multiple factors in the DESeq formula design or subset data to analyze
DESeq2 multiple
3.0 years ago Yijing • 0
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6
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2.5k
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How to extract all comparison in DESeq2 LRT test
DESeq2 Likelihood-ratiotest
3.0 years ago Yijing • 0
0
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13
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3.5k
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DESeq2 design multi factor
DESeq2 design 0substract nofullrank
updated 3.0 years ago by 43k • written 3.1 years ago by ▴ 10
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1
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853
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TOMOseq analysis
DESeq2 tomoda
updated 3.0 years ago by 43k • written 3.1 years ago by • 0
0
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2
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1.3k
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RNA-Seq Reads Count
DESeq2 htseq DEGseq RNASeq read
updated 3.0 years ago by 43k • written 3.1 years ago by • 0
1
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3
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4.4k
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DESeq2/genefilter compatibility with R 4.2.2
DESeq2 genefilter
3.0 years ago Morgane ▴ 10
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4
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1.2k
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Paired analysis model
DESeq2
3.1 years ago • updated 3.0 years ago giulia.lopatriello • 0
1
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1
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1.3k
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Limit the number of nodes in DESeq2
DESeq2 BiocParallel
updated 3.0 years ago by ★ 5.0k • written 3.0 years ago by ▴ 10
2
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1
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1.1k
views
Different sequencing depth between replicates and samples
DESeq2 edgeR DiffBind
updated 3.1 years ago by 53k • written 3.1 years ago by ▴ 10
0
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3
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2.5k
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Differential Expression Analysis on RNAseq - RSEM expected_count from UCSC RNA-Seq toil recompute
DESeq2 Toil RSEM
3.1 years ago Niveditha ▴ 20
1
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4
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3.3k
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plotCounts to visualize variations of a specific genes along conditions
DESeq2 plotCounts vst
updated 3.1 years ago by 43k • written 3.1 years ago by ▴ 10
3
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12
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3.5k
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Replicates in DESeq2
DESeq2
updated 3.0 years ago by • 0 • written 4.3 years ago by ▴ 10
1
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2
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1.5k
views
Design formula with batch effects DESeq2 "Not full rank matrix" error.
DESeq2 BatchEffect RNASeq
updated 3.1 years ago by ★ 1.4k • written 3.1 years ago by • 0
0
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4
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1.1k
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DESeq2 design with continuous variables AND filtering of low counts
DESeq2
updated 3.1 years ago by 43k • written 3.1 years ago by • 0
4,838 results • Page 17 of 97
Recent ...
Replies
Answer: mzR-Rcpp compiler version issue by Laurent Gatto 1.6k
There are two issues here. First, a warning about mzR, that you can safely ignore. It tells you that mzR was compiled using a different …
Comment: Identifying differentially expressed genes in individual samples from a large co by jamie.gearing ▴ 60
Great. Yes, something descriptive is probably good enough, even if the p-values themselves are not so rigorous. Thanks very much Gordon!
Comment: Co-occurrence Network Analysis between Algae and Bacteria by Stefano Mangiola ▴ 40
Just a placeholder, that we are extending `sccomp` to co-occurrence analyses. Yours could be a good use-case to test first. We will be in t…
Answer: DESeq2 design for haplotype MPRA by aimesd808 • 0
I appreciate you telling me about this. Now it's crystal plain to me. Publish this: https://support.bioconductor.org/p/9162649/
Answer: Extract snp information from genomic regions with biomaRt -> "oaries_snp" by Kevin Blighe ★ 4.0k
My sincere apologies that my colleagues had ignored your question. The error occurs because the "chromosomal_region" filter is not valid…
Votes
Answer: Identifying differentially expressed genes in individual samples from a large co
Answer: Identifying differentially expressed genes in individual samples from a large co
Bioconductor Seminar Series - Dec 2: Deep-learning Gene Perturbation Effect Prediction
Comment: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
Comment: Error installing Seqinfo
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Popular Question to shepherl 4.2k
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