Showing : DeSeq2 • reset
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Obtention of the binomial transformed count table with edgeR
DESeq2 edgeR RNASeq DifferentialExpression
updated 2.6 years ago by 53k • written 2.6 years ago by • 0
0
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1
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803
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DESeq2: Comparison between 1 test sample with 1 control sample
DESeq2
updated 2.6 years ago by ★ 5.0k • written 2.6 years ago by • 0
2
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17
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3.4k
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lfcshrink error DESeq2
DESeq2 lfcshrink DESe
updated 2.6 years ago by 43k • written 2.6 years ago by • 0
0
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2
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852
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Deseq2 design
DESeq2 genes Differential expressed
2.6 years ago Syed Zaheer ▴ 10
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2
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1.3k
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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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3
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2.2k
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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
2
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2
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968
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load failed for ‘DESeq2’
DESeq2
updated 2.6 years ago by 4.2k • written 2.6 years ago by ▴ 10
8
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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 2.6 years ago by 43k • written 2.6 years ago by ▴ 90
0
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2
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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
0
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2
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802
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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
0
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1
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597
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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
1
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2
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813
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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
0
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1
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1.0k
views
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
0
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1
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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
1
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2
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900
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Different regions for normalisation
DESeq2 median-of-ratios normalisation
2.6 years ago msrch • 0
0
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2
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1.2k
views
Why my log2fcs are too high?
DESeq2 SingleCell log2FC
2.6 years ago paria.alipour • 0
0
votes
1
reply
815
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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
0
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1
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957
views
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
0
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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
8
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10
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17k
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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
1
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1
reply
726
views
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
1
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1
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1.0k
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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
0
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3
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1.5k
views
remving pseudogenes and lncRNA from deseq2 res
filter deseq2
updated 2.6 years ago by 43k • written 2.6 years ago by • 0
1
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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
0
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1
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742
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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
1
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3
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1.4k
views
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
2
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4
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2.6k
views
How to get TPM / FPKM after batch correction with DESeq2?
DESeq2 BatchEffect tpm fpkm
2.6 years ago vk • 0
2
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2
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1.8k
views
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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1
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3.2k
views
FPKM t-test vs DEseq2
DESeq2 statistics rna-seq
updated 2.6 years ago by ★ 5.0k • written 2.6 years ago by ▴ 10
0
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1
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864
views
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
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
views
DESeq2 for single cell pseudobulk processing
DESeq2
updated 2.6 years ago by 43k • written 2.6 years ago by ▴ 10
0
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1
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767
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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
4
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5
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2.2k
views
Adding cell population estimates as a covariate in DESeq2 differential gene expression analysis
DESeq2 Dese DifferentialRegulation differe
updated 18 months ago by • 0 • written 2.7 years ago by ▴ 10
0
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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 2.7 years ago by • 0
5
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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
1
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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
1
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2
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1.5k
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Removing Unwanted Variations
DESeq2 NanoStringNCTools RUVnormalize RUVSeq DifferentialExpression
2.6 years ago AZ ▴ 30
4
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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
0
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2
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822
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DESeq2 design matrix accounting for high heterogeneity of individuals inside a group
DESeq2
2.7 years ago a.wag • 0
1
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1
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912
views
Can I run deseq2 on two separate experiments at once?
rnaseq deseq2
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by • 0
4
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8
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2.8k
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DESEQ2 - What is the recommended workflow in terms of pre-filtering and counts normalization?
DESeq2 Transcriptomics
updated 2.7 years ago by ★ 13k • written 2.7 years ago by ▴ 20
0
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3
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1.1k
views
How to import dataset from other software into DESeq2?
DESeq2
updated 2.7 years ago by ★ 1.4k • written 2.7 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 2.7 years ago by • 0 • written 2.7 years ago by • 0
0
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1
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670
views
Can a expressed gene dataset yielded after CPM be used in DESeq2 and EdgeR?
DESeq2 edgeR
updated 2.7 years ago by ★ 4.1k • written 2.7 years ago by • 0
0
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1
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508
views
DESeq
DESeq2
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by • 0
3
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6
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1.6k
views
Mistake in Cook's distance calculation in DESeq2 or am I missing something?
DESeq2
2.7 years ago phil.xie • 0
0
votes
2
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732
views
Inverted log2foldchange in study?
DESeq2
updated 2.7 years ago by ▴ 90 • written 2.7 years ago by • 0
4,840 results • Page 13 of 97
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Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: 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
Votes
Upcoming Ensembl API and data access changes - new blog post available
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
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Popular Question to Hervé Pagès 16k
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