Showing : DEseq2 • reset
3
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2
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1.5k
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Using deseq2 with batch effects and classification as downstream analysis
deseq2 batch effect classification
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
0
votes
4
replies
2.2k
views
New computer won't install DESeq2
deseq2 rstudio install error
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
0
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3
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1.7k
views
Strange lfcShrink plot when running DESeq2 workflow
DESeq2 rnaseq rna-seq deseq2 deseq
7.1 years ago Ben ▴ 50
1
vote
7
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5.1k
views
DESEq2 Error in rownames<-(*tmp*, value = names(x))
software error deseq2
updated 7.1 years ago by 43k • written 7.2 years ago by ▴ 20
0
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3
replies
1.8k
views
Reason: image not found Error: package GenomeInfoDb could not be loaded
deseq2 conda
7.1 years ago adam.cribbs ▴ 10
0
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4
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1.3k
views
how to make gene cluster from RNA-Seq counts?
deseq2 rnaseq R
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
2
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5
replies
1.3k
views
DEseq2 - minimum number of genes
DEseq2
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
2
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1
reply
1.3k
views
DeSeq2 batch effect
deseq2
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
2
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4
replies
1.5k
views
DESeq2 design with multiple factors
rnaseq deseq2 multiple factor design
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
2
votes
7
replies
3.3k
views
How to block for a subject in a 2 factor design formula
deseq2 differential gene expression rnaseq
7.1 years ago Onyi Ukay • 0
1
vote
2
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1.6k
views
trouble importing data for DEseq2 workflow
deseq2 tximport tximportdata pasilla Tutorial
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
0
votes
2
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935
views
Approaches for DESeq2 analysis with one factor and many levels
deseq2
7.1 years ago fl ▴ 20
3
votes
8
replies
1.7k
views
DESEQ2 normalize data of population data
deseq2 multiple factor design
updated 7.2 years ago by 43k • written 7.2 years ago by • 0
4
votes
2
replies
3.4k
views
Interpreting the results from lfcShrink() with apeglm in DESeq2
deseq2 apeglm lfcshrink
updated 7.2 years ago by 43k • written 7.2 years ago by ▴ 180
2
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5
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14k
views
Calculating FPKM from raw counts data using fpkm() in deseq2
deseq2 r fpkm() geneexpression
updated 7.2 years ago by 43k • written 7.2 years ago by ▴ 60
0
votes
2
replies
1.7k
views
DESeq2 got stuck for one night, restarting?
deseq2 rnaseq
updated 7.2 years ago by 43k • written 7.2 years ago by ▴ 20
5
votes
7
replies
4.6k
views
Deseq2 design for one condition over 8 different time point
deseq2 rna-seq design matrix deseq
updated 7.2 years ago by 43k • written 7.2 years ago by ▴ 10
0
votes
2
replies
1.0k
views
DESeq2 normalization Factor Matrix to correct for uneven targeted sequencing coverage
deseq2 normalization
updated 7.2 years ago by 43k • written 7.2 years ago by • 0
0
votes
1
reply
5.7k
views
Usage of prepDE.py with stringtie and deseq2
prepDE STRINGTIE deseq2
updated 7.2 years ago by 43k • written 7.2 years ago by ▴ 10
1
vote
1
reply
712
views
Relationship between base mean and adjusted p-value?
deseq2
updated 7.2 years ago by 43k • written 7.2 years ago by • 0
0
votes
2
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2.0k
views
Averaging over biological replicates with DESeq2 for heatmap plotting
deseq2 pheatmap average
updated 7.2 years ago by 68k • written 7.2 years ago by • 0
1
vote
2
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1.3k
views
Quicker way to contrast multiple genotypes with treatment in DeSeq2
deseq2 DeSeq2
updated 7.2 years ago by 43k • written 7.2 years ago by ▴ 10
0
votes
5
replies
1.8k
views
Splitting a dataset and control sample batch
deseq2 interactions batch effect correction grouping variable
updated 7.2 years ago by 43k • written 7.2 years ago by ▴ 110
3
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4
replies
2.5k
views
DGE matrix annotation
DGE DESeq2 AnnotationDbi
updated 7.2 years ago by 68k • written 7.2 years ago by • 0
0
votes
1
reply
846
views
Multiple tissue types in one DESeq2 object
deseq2
updated 7.2 years ago by 43k • written 7.2 years ago by ★ 1.4k
1
vote
3
replies
3.4k
views
deseq2 DESeqDataSet size when saved
deseq2 infrastructure deseqdataset importing
updated 7.2 years ago by 43k • written 7.2 years ago by • 0
0
votes
6
replies
1.7k
views
Custom model matrix for multi factordesign
deseq2 LRT geometric mean estimatesizefactors model.matrix
updated 7.2 years ago by 43k • written 7.2 years ago by • 0
0
votes
6
replies
3.1k
views
Large fold changes after deseq2 when one condition has two zeros and small number the other condition has two zeros and a large number
rnaseq rsem deseq2
7.2 years ago loliveira • 0
1
vote
3
replies
1.1k
views
Deseq2 Interaction Term to catch
deseq2 interaction term
7.2 years ago guipagui • 0
0
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1
reply
1.1k
views
Deseq2 interaction results
deseq2 within-pair analysis
updated 7.2 years ago by 43k • written 7.2 years ago by • 0
1
vote
2
replies
1.5k
views
DESeq2: DESeq2 interaction term study result interpretation
deseq2
updated 7.2 years ago by 43k • written 7.2 years ago by ▴ 10
0
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3
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1.5k
views
DESeq2 group comparison
deseq2 deseq differential binding analysis
updated 7.2 years ago by 43k • written 7.2 years ago by ▴ 60
0
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8
replies
1.2k
views
Duplication of same sample as if two different samples
deseq2
updated 7.2 years ago by 43k • written 7.2 years ago by ▴ 60
2
votes
6
replies
1.6k
views
DESeq2 Gene Expression Set up: Behavior vs Age
deseq2 experimental design
updated 7.2 years ago by 43k • written 7.2 years ago by • 0
2
votes
4
replies
2.7k
views
why the logFC is different between edgeR,DESeq2 results and fpkm logFC(log2(FPKM_tumor_mean/FPKM_normal_mean)?
deseq2 edger fpkm counts fc
updated 7.2 years ago by 53k • written 7.2 years ago by • 0
1
vote
2
replies
1.7k
views
how to output and get the normalization gene expression data (similar to the FPKM gene expression data) from reads count data by DESeq2 and edgeR?
deseq2 edger fpkm counts TCGA
updated 7.2 years ago by 53k • written 7.2 years ago by • 0
0
votes
5
replies
1.9k
views
RNA-seq time course experiment - DESEq2 Contrasts
deseq2 rna-seq interactions contrast
updated 7.2 years ago by 43k • written 7.2 years ago by ▴ 10
0
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9
replies
3.2k
views
DESEQ2 / Phyloseq contrasts no longer work as before following update
deseq2 phyloseq
7.2 years ago eoin • 0
1
vote
2
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1.7k
views
DESeq2 design nested or time course
deseq2 nested design
updated 7.2 years ago by 43k • written 7.2 years ago by • 0
0
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0
replies
950
views
Changing vertical scale to linear for expression reporting of DESeqDataSet
reportingtools deseq2
7.2 years ago trebbiano • 0
2
votes
4
replies
1.8k
views
RNA-seq time course experiment - LRT design hep
deseq2 lrt timecourse
7.2 years ago Maithê Barros ▴ 10
0
votes
2
replies
975
views
DESerq2 older releases
deseq2 release
updated 7.2 years ago by 43k • written 7.2 years ago by ▴ 150
1
vote
5
replies
1.1k
views
can i only analyse some genes different RNAseq expression analyse not the whole transcriptome RNAseq analyse by DESeq2 or edgeR
deseq2 edger
updated 7.2 years ago by 53k • written 7.2 years ago by • 0
0
votes
2
replies
2.0k
views
DESeq2 batch correction and possible ComBat/SVA over-correction of RNA-seq data
deseq2 combat sva rna-seq
updated 7.2 years ago by 43k • written 7.2 years ago by • 0
2
votes
4
replies
4.7k
views
DESeq2- Size factors (median of ratios) assumptions - global adjustment normalization?
deseq2 quantro normalization
7.2 years ago Victor Barrera • 0
0
votes
1
reply
2.3k
views
Counting exonic and intronic reads for differential gene expression
deseq2 intron
updated 7.2 years ago by ★ 1.6k • written 7.2 years ago by ▴ 40
0
votes
5
replies
1.3k
views
Dealing with low read count in early time point samples
deseq2
updated 7.2 years ago by 43k • written 7.2 years ago by • 0
2
votes
5
replies
3.1k
views
Visualise and remove batch effects in DESeq2
deseq2 rnaseq
updated 7.2 years ago by 43k • written 7.2 years ago by • 0
0
votes
3
replies
554
views
Extracting normalized count data from DESeq2
deseq2
updated 7.2 years ago by 43k • written 7.2 years ago by • 0
0
votes
2
replies
2.7k
views
Different p-value using input files with pairwise and multiple condition design
deseq2
updated 7.2 years ago by 43k • written 7.2 years ago by • 0
4,840 results • Page 59 of 97
Recent ...
Replies
Comment: 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
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.
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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