Showing : Deseq2 • reset
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DESeq2 package unrecognized after downloading latest version of R: keep getting erros
DESeq2
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
0
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1
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833
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Design formula for genotype-specific condition effects using ~group in the design
RNASeqData DifferentialExpression DESeq2
updated 2.4 years ago by 43k • written 2.4 years ago by • 0
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5
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1.3k
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Wondering how to look at the reads of a gene in samples to check if it was knocked out?
knockout DESeq2
written 2.4 years ago by • 0
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4
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1.5k
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DESEq2 Error: rows did not converge
DESeq2
2.4 years ago andrebolerbarros ▴ 20
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2
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1.1k
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Can DESeq2 handle low number of samples and replicates?
DESeq2
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
2
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5
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2.3k
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DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 19 months ago by • 0 • written 2.4 years ago by • 0
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4
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1.6k
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Problem in running DESeq from expected count data of Transcriptome by Trinity followed by RSEM
Tissue Spati RSEM deno DEseq2
written 2.5 years ago by • 0
1
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3
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1.2k
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DESeq: relaxing gene filtering thresholds increases mean-Sd correlation, but recovers many important genes
metaanalysis meanSd genefilter DESeq2
2.4 years ago Ndimensional ▴ 20
2
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8
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1.9k
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Failure of beta estimates to converge in DESeq2 despite noncollinearity and reasonable counts
converge beta DESeq2
2.4 years ago Ndimensional ▴ 20
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5
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1.4k
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Model and Contrasts with 4 variables
contrast edgeR DESeq2
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
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1
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513
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Is there a way to solve "the model matrix is not full rank", when just one of my sample is showing batch effect?
DESeq2
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
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17
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4.9k
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What causes this DESeq2 error at "fitting model and testing"?
deseq2 differential expression error
updated 2.4 years ago by • 0 • written 8.1 years ago by • 0
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1
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723
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DESeq2 how to extract expression values corresponding to log2FoldChange
DESeq2
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
0
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1
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800
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Comparing DGE between datasets with uneven sample sizes using DESeq2
unevensamplesizes ComparingDGEresults DESeq2
updated 2.4 years ago by 43k • written 2.4 years ago by • 0
1
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1
reply
711
views
Deseq contrast question
RNASeqData DESeq2
updated 2.4 years ago by 43k • written 2.4 years ago by ▴ 10
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4
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1.2k
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Using different filtering steps in different iterations of DEseq2
DESeq2
2.4 years ago marinaw ▴ 20
1
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2
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923
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Individual DESeq2 runs versus a single DESeq2 run with contrasts produce different results
contrasts DESeq2
2.4 years ago jovel_juan ▴ 30
0
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2
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1.1k
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Can DESeq2 handle huge variations in sequencing depth among samples?
HugevariationsinsequencingDepth DESeq2
2.4 years ago Gopinath • 0
0
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4
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2.0k
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Discrepancy between DESeq2 files produced in Galaxy and R(RStudio)
DESeq2
updated 21 months ago by • 0 • written 2.4 years ago by • 0
0
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1
reply
609
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Several questions about the workflow using DESeq2 to process RNA data
DESeq2
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by ▴ 20
1
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3
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4.9k
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DeSEQ 2 Error: some values in assay are negative
Countmatrix negativeassay DESeq2
2.4 years ago dania.khalid • 0
2
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2
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1.4k
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DESeq2 on multilevel design variable
DESeq2
updated 2.4 years ago by ★ 1.4k • written 2.4 years ago by • 0
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1
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1.1k
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DESeq2 + analysis question for design with uneven time point design
timecourse KEGG DESeq2
updated 2.4 years ago by 43k • written 2.5 years ago by • 0
0
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2
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2.3k
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Handling NA's in Deseq2
Dese DESeq2
2.4 years ago Asger Mølgaard • 0
0
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2
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1.3k
views
Remove duplicate genera in DEseq output?
DESeq2
updated 2.4 years ago by ▴ 760 • written 2.4 years ago by • 0
0
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2
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1.5k
views
Can VST-transformed community composition data be expressed as relative abundance?
vst relativeabundance Normalization DESeq2
2.5 years ago • updated 2.4 years ago dwas • 0
3
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6
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1.6k
views
Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 2.5 years ago by 53k • written 2.5 years ago by ▴ 10
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2
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1.0k
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Normalized counts from LRT or Wald test?
DESeq2
updated 2.5 years ago by ★ 5.0k • written 2.5 years ago by • 0
2
votes
1
reply
879
views
DESeq2 or edgeR for Presence and Absence of Proteins
edgeR DESeq2
updated 2.5 years ago by ★ 5.0k • written 2.5 years ago by • 0
0
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2
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1.3k
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DoparParam() execution fails when foreach() works
clustermq doparallel DESeq2
2.5 years ago boris • 0
0
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2
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1.8k
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Nanostring data differential expression analysis: limma or DESeq2?
DESeq2 NanoStringDiff limma
2.5 years ago pg45863 ▴ 10
0
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1
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1.0k
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how to solve this error
DESeq2 GEO miRNAData
updated 2.5 years ago by ★ 5.0k • written 2.5 years ago by • 0
0
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4
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1.4k
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problem while retriving the genes by using p value and log2fc as conditions
Bioconductor Transcriptomics DifferentialExpression DESeq2
2.5 years ago sreeshmaraj72 • 0
0
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1
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967
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DESeq2 about comparasion of gene expression change on two-time points between two group samples.
DESeq2 RNASeqData edgeR limma DifferentialExpression
updated 2.5 years ago by ★ 1.4k • written 2.5 years ago by • 0
2
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9
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7.0k
views
how to control age and gender effect in expression data using DESeq2
deseq2 rnaseq mirna-seq differential gene expression
written 7.7 years ago by ▴ 10
3
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3
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1.9k
views
Subsetting DESeq data set to compare treatments within one group (multi-group experiment)
DifferentialExpression DESeq2
updated 2.5 years ago by ★ 1.4k • written 2.5 years ago by ▴ 20
1
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2
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1.8k
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Batch effect between biological replicates
BatchEffect DESeq2
2.5 years ago gtechbio ▴ 10
1
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3
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1.1k
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Find if one gene has a significantly different Log2FC than a different gene
DESeq2
updated 2.5 years ago by 43k • written 2.5 years ago by • 0
0
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3
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1.3k
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Dispersion outliers genes
Dispersion DESeq2
2.5 years ago raya.fai ▴ 60
0
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1
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1.2k
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Which file in tximport should I use for DESeq2 analysis?
tximport DESeq2
updated 2.5 years ago by 68k • written 2.5 years ago by • 0
0
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2
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1.9k
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about baseMean in DEseq2
DESeq2
written 4.3 years ago by ▴ 670
3
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3
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1.4k
views
Rlog performed on tpm or raw transcript abundances?
DESeq2 rlog
written 2.9 years ago by • 0
0
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2
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1.1k
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Accounting for technical replicates in DESeq2
DESeq2
updated 2.5 years ago by ★ 1.4k • written 2.5 years ago by • 0
3
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1
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1.0k
views
Applying DESeq2 to (suspected) Poisson distributed gene expression data (in the case of pseudoreplication)
DESeq2
updated 2.5 years ago by 43k • written 2.5 years ago by • 0
2
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1
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1.4k
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scaledTPM for DESeq2 using tximport
DESeq2 tximport
updated 2.5 years ago by 43k • written 2.5 years ago by • 0
2
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7
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3.0k
views
optimHess problem in apeglm/DESeq2
DESeq2 apeglm
updated 2.5 years ago by 43k • written 2.5 years ago by ★ 5.0k
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2
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1.1k
views
Obtention of the binomial transformed count table with edgeR
DESeq2 edgeR RNASeq DifferentialExpression
updated 2.5 years ago by 53k • written 2.5 years ago by • 0
0
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1
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799
views
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
2
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17
replies
3.4k
views
lfcshrink error DESeq2
DESeq2 lfcshrink DESe
updated 2.5 years ago by 43k • written 2.5 years ago by • 0
0
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2
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842
views
Deseq2 design
DESeq2 genes Differential expressed
2.5 years ago Syed Zaheer ▴ 10
4,836 results • Page 12 of 97
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Comment: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif by Matthew Thornton ▴ 380
WOW! Thank you so much for the information. I will do this.
Comment: "Watched Tags" are being erased rather than updated by RalphSavage99 • 0
Thanks for sharing https://github.com/Bioconductor/support.bioconductor.org/issues/112
Answer: Add additional maintainer for MOFA2 by shepherl 4.2k
These requests are best on the bioc-devel @ r-project.org or a request to maintainer @ bioconductor.org -- We would ideally need the curre…
Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hi Rui Tang, The "buffer overflow detected" error in featureCounts usually stems from a corrupted or malformed GTF file, often due to tr…
Answer: Problem with the TMB plot by Kevin Blighe ★ 4.0k
Hi, The linear TMB plot with no clustering suggests your variant calls may lack sample-specific discrimination, likely due to filtering ap…
Votes
Answer: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
Using edgeR or DESeq2 to analyze allele-specific expression?
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
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