0
votes
1
reply
644
views
DESeq2 for comparisons within group
deseq2 interaction factors complex design
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
2
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3
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Boxplot function not showing all reads length on x-axis
boxplot reads fastq sequencing rsubread
updated 6.7 years ago by ★ 3.6k • written 6.7 years ago by ▴ 60
0
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1
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948
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Error while running PCA on 1.3 Million Brain Cells from E18 Mice
software error
6.7 years ago bsharmi6 • 0
0
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0
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766
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Number of profiles in JASPAR2018
JASPAR2018
6.7 years ago capricygcapricyg ▴ 10
2
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2
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topGO package unable to find library(ALL) and data(ALL)
topGO software error
updated 6.7 years ago by 68k • written 6.7 years ago by ▴ 60
1
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2
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DiffBind returns empty consensus peakset
DiffBind consensus
updated 6.7 years ago by ★ 5.2k • written 6.7 years ago by • 0
1
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4
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cn.mops on CRAM files
cn.mops
updated 6.7 years ago by ▴ 540 • written 6.7 years ago by • 0
0
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1
reply
621
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Test genes expressed ( not just expressed higher ) in one or two group
limma edger
updated 6.7 years ago by 53k • written 6.7 years ago by ▴ 30
0
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1
reply
911
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Using already normalized counts
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updated 6.7 years ago by ★ 13k • written 6.7 years ago by • 0
0
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0
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724
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Incompatible phenoData object error in ReadqPCR package
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6.7 years ago jchoza • 0
4
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1
reply
1.4k
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Print Differentially Expressed Exons From Dexseq Results
DEXSeq RNA-Seq
updated 6.7 years ago by ★ 1.9k • written 6.7 years ago by ▴ 10
2
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6
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DESeq2 analysis of no-normalized data yielded biased results
deseq2 normalization
6.7 years ago Victor Chano • 0
0
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3
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1.6k
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rbind VCF Two Objects Column Names Error
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6.7 years ago Dario Strbenac ★ 1.6k
4
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2
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2.5k
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single cell data: adding random effects for subject with multilevel experiment design
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updated 6.7 years ago by ★ 29k • written 6.7 years ago by • 0
1
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3
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2.2k
views
genbankr not working because rtracklayer does not install
genbankr rtracklayer
updated 3.1 years ago by • 0 • written 6.7 years ago by • 0
0
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6
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2.2k
views
how to set offset matrix to Deseq2 differential analysis
deseq2 Kallisto tximport
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
0
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0
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1.1k
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Job: Post-Doctoral Research Fellow, Cancer Genomics (Fred Hutch - Seattle, WA)
job seattle Job
6.7 years ago Fred Hutch (Recruiting) ▴ 40
4
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6
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1.2k
views
Limma model design: is it better to just build a separate design for each specific comparison?
limma
updated 6.7 years ago by 68k • written 6.7 years ago by ▴ 60
14
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21
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13k
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Installing ShortRead - error: zlib not found even with zlib in LD_LIBRARY_PATH
package installation shortread dependency
updated 6.7 years ago by ▴ 240 • written 7.7 years ago by ▴ 60
10
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20
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27k
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Batch Effect in DESeq2, how to control, how to remove it, how to address biological question
deseq2 batch effect batch
updated 16 months ago by 68k • written 6.7 years ago by ▴ 30
0
votes
0
replies
1.1k
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Gviz colour reads by Read Group in AlignmentTrack
gviz igv
6.7 years ago ido.idobar • 0
0
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0
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1.2k
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Job: Bioinformatics Analyst II, Genomics Shared Resource (Fred Hutchinson Cancer Research Center Seattle, WA)
jobs seattle bioinformatics Job
6.7 years ago Fred Hutch (Recruiting) ▴ 40
1
vote
2
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1.3k
views
"hgu133plus2db" package not working in R
microarray affy annotation
updated 6.7 years ago by 68k • written 6.7 years ago by • 0
5
votes
3
replies
1.8k
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Steep dendrograms and few modules. WGCNA on RNA seq data
RNA seq wgcna
updated 6.7 years ago by ★ 3.0k • written 6.7 years ago by ▴ 20
0
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1
reply
1.4k
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Assesing genomic segment enrichment with GenomicRanges (R-package)
GenomicRanges R genomic enrichment
updated 6.7 years ago by ★ 11k • written 6.7 years ago by • 0
0
votes
3
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952
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Salmon / tximport
tximport deseq2
updated 6.7 years ago by 43k • written 6.7 years ago by ▴ 10
0
votes
10
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3.5k
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Error in reading data on isoformswitchanalyzeR
isoformswitchanalyzeR rna-seq splice-variants
written 6.8 years ago by • 0
3
votes
3
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2.2k
views
Using alternative LFC shrinkage methods for computing p-values in DESeq2
deseq2 apeglm statistics
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
2
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1
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1.3k
views
Multiple groups and two methods to analyse them with DESeq2
deseq2
updated 6.7 years ago by 43k • written 6.7 years ago by ▴ 30
0
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1
reply
1.4k
views
Comparing transcriptome variation across groups after Variance stabilizing transformation using DESeq2
deseq2 vst variance
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
2
votes
5
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2.0k
views
Does `clusterCTSS` and `aggregateTagClusters` sum raw-tag counts (and tpm) of the clustered tags into the resultant cluster?
CTSS clustering tag per million tag counts CAGEr
updated 4.2 years ago by ▴ 180 • written 6.7 years ago by • 0
0
votes
3
replies
1.1k
views
Sanity Checking Mixed Factorial Proteomics Analysis Workflow Using Limma
limma
updated 6.7 years ago by 53k • written 6.7 years ago by • 0
1
vote
2
replies
2.8k
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FDR and mixed FDR in limma fry()
limma FDR
updated 6.7 years ago by 53k • written 6.7 years ago by • 0
0
votes
15
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3.9k
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Is the STRINGdb server down?
STRINGdb R protein
updated 6.7 years ago by • 0 • written 6.9 years ago by • 0
2
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5
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1.5k
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Software package for RNA-seq reads simulation?
rna-seq reads
updated 6.7 years ago by 53k • written 6.7 years ago by ▴ 100
5
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5
replies
3.2k
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Principal components in DESeq2
deseq2
6.7 years ago Mozart ▴ 30
0
votes
2
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848
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How to transform chromosome start end to band in batch using biomaRt
software error
updated 6.7 years ago by 68k • written 6.7 years ago by • 0
0
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2
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979
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Can EDGE analyse RNA-seq data?
edge RNA-seq
updated 6.7 years ago by 68k • written 6.7 years ago by • 0
0
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3
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How to find number of patients (percentage of given population) having high expression of gene A in given microarray data ?
microarray r clustering high expressed genes
updated 6.7 years ago by 68k • written 6.7 years ago by • 0
0
votes
6
replies
2.9k
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Save ExpressionSet to csv file with columns and rows headers
microarray genefilter
updated 6.7 years ago by 68k • written 6.7 years ago by ▴ 10
2
votes
1
reply
2.3k
views
Using SVA (surrogate variable analysis) to correct for 'completely' confounded cell type composition in DNA methylation data
sva linear model cell type composition R microarray
6.7 years ago epibio ▴ 10
0
votes
1
reply
1.2k
views
Help running the nondetects::qpcrImpute on my data?
nondetects qpcrImpute
updated 6.7 years ago by ▴ 830 • written 6.9 years ago by • 0
0
votes
0
replies
833
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Error with HTqPCR rbind
HTqPCR
6.7 years ago NAIARA GARCÍA ▴ 10
5
votes
7
replies
3.9k
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logCPM to CPM conversion after removeBatchEffect()
edger removeBatchEffect cpm logCPM limma
6.7 years ago altintas.ali • 0
0
votes
0
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1.3k
views
Job: Post-doctoral Fellow - Aparicio Lab @ BC Cancer Research Center, Vancouver BC Canada
single cell genome cancer Job
6.7 years ago jmaanaki • 0
1
vote
3
replies
2.3k
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Troubles with barcodeRanks()
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updated 6.7 years ago by ★ 29k • written 6.7 years ago by ▴ 170
1
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3
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1.9k
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DMRcate liftover to grch38
hg19 liftover matrixeqtl DMRcate
updated 6.7 years ago by 68k • written 6.7 years ago by ▴ 10
0
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2
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4.6k
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Reading peaks from MACS2 with DiffBind
chip-seq peak calling diffbind
updated 18 months ago by ▴ 20 • written 6.7 years ago by • 0
2
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2
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DiffBind's MA plots for ChIP-seq - how to properly interpret normalization from them?
diffbind R MAplot Chipseq
updated 6.7 years ago by ★ 5.2k • written 6.7 years ago by ▴ 10
0
votes
2
replies
1.1k
views
can TissueEnrich be used to calculate the tissue-specific lncRNAs in plants?
TissueEnrich
updated 6.7 years ago by ▴ 10 • written 6.7 years ago by • 0
46,741 results • Page 210 of 935
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Answer: Limma-voom sample weights and impact on DEG numbers by fawadsaafir • 0
<a href="https://deltaexecutoor.com/">delta apk</a> también conocido como Delta X, es una herramienta avanzada para ejecutar scripts perso…
Comment: Error message that there is no package called Biobase by DamionLedner99 • 0
thanks for sharing!!! https://cran.r-project.org/
Comment: msmsTests, inconsistent sign between lFC.Av and LogFC by Ben • 0
Continued here due to posting difficulties: Extract from the results table: ``` Inhibitor Vehicle lFC.Av LogFC ... F1 0.0 27…
Answer: DESeq2 for 16S rRNA Analysis by James W. MacDonald 68k
The Wald test is only meant for comparison of two groups at a time, so it depends on what you mean by 'analyze across multiple groups at a …
Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list' by varying.mastodon.isyn • 0
Oh, that error! I remember wrestling with that one for hours when I was first learning Python. Turns out I was trying to use a list itself …
Votes
Answer: What happens to genes with low dispersion during dispersion shrinkage in DESeq2
Comment: Are transformed values from rlog /vst log2 normalized counts?
Answer: Are transformed values from rlog /vst log2 normalized counts?
A: DESeq2 normalization vs VST vs rlog
Answer: How to directly decet the outlier samples (libraries) in EdgeR pipeline
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