Showing : DEseq2 • reset
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DESeq2: Comparison between 1 test sample with 1 control sample
DESeq2
updated 2.5 years ago by ★ 5.0k • written 2.5 years ago by • 0
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17
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lfcshrink error DESeq2
DESeq2 lfcshrink DESe
updated 2.5 years ago by 43k • written 2.6 years ago by • 0
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2
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849
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Deseq2 design
DESeq2 genes Differential expressed
2.6 years ago • updated 2.5 years ago Syed Zaheer ▴ 10
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DESeq: low p-values for genes with zero counts in all but one sample of the compared groups
DESeq2 DifferentialExpression
2.6 years ago António Miguel de Jesus Domingues ▴ 510
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DESeq2 1.40.0 binary install issue on Mac M1 (Bioconductor 3.17)
DESeq2
written 2.6 years ago by ▴ 10
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3
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1.9k
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Can i perform DEseq2 from 2 different rse objects download from RECOUNT database
DESeq2 recount GTEx TCGA recount3
updated 2.6 years ago by ★ 5.0k • written 2.6 years ago by ▴ 20
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2
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load failed for ‘DESeq2’
DESeq2
updated 2.6 years ago by 4.2k • written 2.6 years ago by ▴ 10
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12
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3.8k
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DESeq2 1.40.0 binary install issue on macOS x86 (Bioconductor 3.17)
DESeq2
updated 2.5 years ago by 43k • written 2.6 years ago by ▴ 90
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2.5k
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model matrix not full rank
DESeq2 RNASeq
updated 2.6 years ago by • 0 • written 2.6 years ago by • 0
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2
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798
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ANOVA-like testing for bulkRNAseq with three conditions with Wald test
DESeq2
updated 2.6 years ago by ★ 5.0k • written 2.6 years ago by • 0
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596
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calculating effect of condition taking into account patient origin and clone_origin
DESeq2
updated 2.6 years ago by 43k • written 2.6 years ago by • 0
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809
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Wondering if DESeq2 is appropriate for PhIP-seq data?
DESeq2 PhIP-seq
2.6 years ago • updated 2.5 years ago Samantha • 0
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1.0k
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What is the correct way to split genex_high and genex_low groups for DE analysis?
DESeq2 RNASeq
updated 2.6 years ago by 43k • written 2.6 years ago by • 0
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1.5k
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DESeq2 Results and Alpha questions
DESeq2
updated 2.6 years ago by 43k • written 2.6 years ago by • 0
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895
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Different regions for normalisation
DESeq2 median-of-ratios normalisation
2.6 years ago msrch • 0
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2
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1.2k
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Why my log2fcs are too high?
DESeq2 SingleCell log2FC
2.6 years ago paria.alipour • 0
0
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1
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814
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Performing pair-wise comparisons for smaller p value analyzing time series data using deseq2
DESeq2
updated 2.6 years ago by ★ 5.0k • written 2.6 years ago by • 0
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1
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952
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DESeq2 design formula
DESeq2
updated 2.6 years ago by ★ 1.4k • written 2.6 years ago by • 0
1
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4
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2.2k
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Merging samples from different sequencing runs
DESeq2
2.7 years ago • updated 2.5 years ago Zainab ▴ 20
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2
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1.4k
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GenomicRanges coult not be loaded after R upgrade
DESeq2 Bioconductor GenomicRanges
updated 2.6 years ago by • 0 • written 2.6 years ago by • 0
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10
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GSEA preranked analysis downstream of DEseq2
deseq2 gsea rnaseq
updated 7 months ago by ★ 5.0k • written 9.3 years ago by ▴ 20
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721
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Using R to measure differential gene expression of one gene due to different treatments using RNASeq counts
DESeq2 edgeR RNAseq
updated 2.6 years ago by 53k • written 2.6 years ago by • 0
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RNA-seq data collected at differnt time points
DESeq2
updated 2.6 years ago by ★ 5.0k • written 2.6 years ago by • 0
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3
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remving pseudogenes and lncRNA from deseq2 res
filter deseq2
updated 2.6 years ago by 43k • written 2.6 years ago by • 0
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2
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1.3k
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summarizeToGene in tximeta causing vastly different results
DESeq2 deseq txime tximeta
updated 2.6 years ago by 43k • written 2.6 years ago by • 0
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739
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Time change in expression vs time change in phenotype
Transcriptomics ExpressionData DESeq2
updated 2.6 years ago by 43k • written 2.6 years ago by • 0
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3
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1.4k
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fc value in ggmaplot does not correspond to the real lfc value on the plot
DESeq2 ggmaplot
updated 2.6 years ago by ★ 5.0k • written 2.6 years ago by • 0
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4
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2.6k
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How to get TPM / FPKM after batch correction with DESeq2?
DESeq2 BatchEffect tpm fpkm
2.6 years ago vk • 0
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2
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1.8k
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Error in checkFullRank(modelMatrix)
DESeq2 BatchEffect DifferentialExpression
updated 2.6 years ago by ★ 5.0k • written 2.6 years ago by ▴ 30
1
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3.2k
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FPKM t-test vs DEseq2
DESeq2 statistics rna-seq
updated 2.6 years ago by ★ 5.0k • written 2.6 years ago by ▴ 10
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861
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Can I use baseMean (from DESeq2) as part of presenting/ interpreting results
DESeq2 diferentialabundance 16srRNA baseMean
updated 2.6 years ago by 43k • written 2.6 years ago by • 0
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4
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1.0k
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Down weighing an outlier in DESeq2 ?
DESeq2
updated 2.6 years ago by ★ 5.0k • written 2.6 years ago by • 0
6
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6
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5.3k
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DESeq2 for single cell pseudobulk processing
DESeq2
updated 2.5 years ago by 43k • written 2.6 years ago by ▴ 10
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765
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Differential express genes in one group across all time points
DESeq2 edgeR BP4RNAseq ensemblVEP
updated 2.6 years ago by 43k • written 2.6 years ago by • 0
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5
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2.2k
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Adding cell population estimates as a covariate in DESeq2 differential gene expression analysis
DESeq2 Dese DifferentialRegulation differe
updated 17 months ago by • 0 • written 2.6 years ago by ▴ 10
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3
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1.7k
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Differential Expression Analysis between Clusters
DESeq2
updated 2.6 years ago by • 0 • written 2.6 years ago by • 0
5
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4.7k
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How to combine two DESeq2 objects (dds) for analysis
DESeq2
updated 2.6 years ago by 43k • written 2.7 years ago by ▴ 10
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5
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2.9k
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How many parameters should be included in the model design for deseq2?
DESeq2 variancePartition
2.7 years ago • updated 2.6 years ago Weiqian ▴ 10
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1.5k
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Removing Unwanted Variations
DESeq2 NanoStringNCTools RUVnormalize RUVSeq DifferentialExpression
2.6 years ago AZ ▴ 30
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2
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3.8k
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Normalisation of data using DESeq2 with multi-groups
DEseq2
2.6 years ago Changsuk ▴ 10
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2
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820
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DESeq2 design matrix accounting for high heterogeneity of individuals inside a group
DESeq2
2.6 years ago a.wag • 0
1
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906
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Can I run deseq2 on two separate experiments at once?
rnaseq deseq2
updated 2.6 years ago by ★ 5.0k • written 2.6 years ago by • 0
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8
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DESEQ2 - What is the recommended workflow in terms of pre-filtering and counts normalization?
DESeq2 Transcriptomics
updated 2.6 years ago by ★ 13k • written 2.6 years ago by ▴ 20
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3
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How to import dataset from other software into DESeq2?
DESeq2
updated 2.6 years ago by ★ 1.4k • written 2.6 years ago by • 0
2
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3
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3.2k
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RNA-seq analysis without replicates
DESeq2 RESEQ RNASeqData
updated 2.6 years ago by • 0 • written 2.6 years ago by • 0
0
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1
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667
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Can a expressed gene dataset yielded after CPM be used in DESeq2 and EdgeR?
DESeq2 edgeR
updated 2.6 years ago by ★ 4.1k • written 2.6 years ago by • 0
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504
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DESeq
DESeq2
updated 2.6 years ago by ★ 5.0k • written 2.6 years ago by • 0
3
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6
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1.6k
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Mistake in Cook's distance calculation in DESeq2 or am I missing something?
DESeq2
2.6 years ago phil.xie • 0
0
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2
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726
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Inverted log2foldchange in study?
DESeq2
updated 2.6 years ago by ▴ 90 • written 2.6 years ago by • 0
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1
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697
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DESeq2 statistical model construction
DESeq2
updated 2.6 years ago by ★ 1.4k • written 2.6 years ago by ▴ 20
4,839 results • Page 13 of 97
Recent ...
Replies
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.
Comment: upstream git branches of bioc-release by Jeroen ▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
Comment: Large logFC but somewhat high FDR by Gordon Smyth 53k
I don't know what `tp1` is. The relevant histogram would be: ``` hist(fit2$p.value[,"KO_vs_WT"]) ```
Answer: p.adjust BH Question by Gordon Smyth 53k
Duplicate of https://support.bioconductor.org/p/41077/
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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