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0
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1.0k
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Concatenating different runs from the same pool of barcoded CyTOF samples
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5.8 years ago mikhael.manurung ▴ 280
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2
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edger
updated 5.8 years ago by 53k • written 5.9 years ago by • 0
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Issues loading a BAM file resulted from featurecounts
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5.9 years ago Konstantinos Yeles ▴ 90
1
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2
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BATCH EFFECT OF AGE
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updated 5.9 years ago by 43k • written 5.9 years ago by ▴ 60
5
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10
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tximport and stevia, how to build tx2gene without any reference genome
deseq2 annotation
updated 5.9 years ago by 43k • written 5.9 years ago by ▴ 60
0
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0
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792
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MAIT metabolomics analysis error
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5.9 years ago YL • 0
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DESeq2 result extraction
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0
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0
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534
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DESeq2 analysis with scaled continues variables
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5.9 years ago adR ▴ 40
1
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1
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974
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DESeq2 paired test (for most samples)
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updated 5.9 years ago by 43k • written 5.9 years ago by • 0
1
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9
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2.1k
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Wrong results of DESeq compared to DESeq2 for some test cases?
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updated 5.9 years ago by ★ 3.8k • written 5.9 years ago by • 0
7
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16
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How to extract phastcons score for all protein coding genes and lncRNAs using GenomicScores?
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updated 14 months ago by • 0 • written 5.9 years ago by ▴ 120
0
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1
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1.5k
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can't library hgu133plus2cdf
hgu133plus2cdf
5.9 years ago 1142985358 • 0
0
votes
6
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947
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Why so few genes are returned?
deseq2
updated 5.9 years ago by ★ 4.0k • written 5.9 years ago by • 0
0
votes
0
replies
959
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Error on FindOptimalBinning function
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5.9 years ago pavel.granalacant • 0
4
votes
2
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6.5k
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DESeq2 Multiple Conditions: Do I need a "reference"?
deseq2
updated 5.9 years ago by ★ 4.0k • written 5.9 years ago by ▴ 10
1
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2
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1.4k
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The coordinate system problem about DiffBind output
diffbind Rory Stark coordinate
updated 5.9 years ago by ★ 5.2k • written 5.9 years ago by ▴ 40
3
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2
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1.5k
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Some confuse about the DBA_SCORE_TMM_READS_EFFECTIVE_CPM in DiffBind
diffbind CPM TMM
updated 5.9 years ago by ★ 5.2k • written 5.9 years ago by ▴ 40
1
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2
replies
799
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Diffbind- results different every time I run it
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updated 5.9 years ago by ★ 5.2k • written 5.9 years ago by • 0
1
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DiffBind in depth explanation
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updated 5.9 years ago by ★ 5.2k • written 5.9 years ago by • 0
2
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3
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1.4k
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Drug response pre- and post-treatment between timepoints across conditions
RNA-seq Paired design Timecourse Diagnosis Covariates
updated 5.9 years ago by ★ 4.0k • written 5.9 years ago by • 0
0
votes
0
replies
1.3k
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WGCNA for Dose-Response RNA-Seq Data
wgcna network analysis
5.9 years ago jwilliamblamer • 0
1
vote
3
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1.6k
views
Design DESeq2 with one or more continues variables
deseq2
5.9 years ago adR ▴ 40
2
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2
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2.1k
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Specific KEGG.db pathways not found in KEGG.db package
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updated 5.9 years ago by 68k • written 5.9 years ago by ▴ 20
6
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9
replies
6.0k
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Centering and scaling numeric variables
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updated 5.9 years ago by ▴ 40 • written 5.9 years ago by ▴ 30
0
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0
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1.3k
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plotting Signalling Pathways using SPIA
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5.9 years ago Assa Yeroslaviz ★ 1.5k
0
votes
5
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2.7k
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biomaRt getBM() returns nothing most of the times
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updated 5.9 years ago by ★ 1.4k • written 5.9 years ago by • 0
0
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4
replies
771
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How to know what genes are differentially expression in DESeq2 simulation?
deseq2
updated 5.9 years ago by ★ 4.0k • written 5.9 years ago by • 0
2
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4
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Quality control in SingleCellExperiment
SingleCellExperiment scater sce quality control
updated 5.0 years ago by • 0 • written 5.9 years ago by • 0
0
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1
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387
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Choosing DESeq2 design
deseq2
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
0
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1
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get Gene ID from GEO microarray dataset with fData
GEO
updated 5.9 years ago by 68k • written 5.9 years ago by • 0
0
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tximport lose transcript names with Salmon bootstrap
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updated 5.9 years ago by • 0 • written 5.9 years ago by • 0
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DE analysis outlier removal
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updated 5.9 years ago by 43k • written 5.9 years ago by • 0
0
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1
reply
745
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TxDb.Hsapiens.UCSC.hg38.knownGene immunoglobulin
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updated 5.9 years ago by 16k • written 5.9 years ago by • 0
0
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5
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updated 9 months ago by • 0 • written 5.9 years ago by • 0
0
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Assay choice for cell type annotation using SingleR when batch effect present in profile
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updated 5.9 years ago by ★ 29k • written 5.9 years ago by ▴ 70
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updated 5.9 years ago by 53k • written 5.9 years ago by ▴ 20
1
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12
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negative one "-1" values in index files using Rsubread
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updated 5.9 years ago by ▴ 450 • written 5.9 years ago by • 0
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917
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DESeq dispersion parameter
deseq2
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
0
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2
replies
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phyloseq_to_deseq2 design strategy for multiple factors analysis (2 or more)
deseq2
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
2
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Joint pathway Analysis using both gene and metabolite data sets
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5.9 years ago emisecherre • 0
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DESeq2 pairwise comparisons w/ 3 factors
deseq2
updated 5.9 years ago by 43k • written 5.9 years ago by ▴ 10
0
votes
1
reply
612
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DiffBind 2.10.0: Consensus peaks seems to miss 2/3 of original sample peaks
DiffBind Consensus peak
updated 5.9 years ago by ★ 5.2k • written 5.9 years ago by • 0
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DiffBind: error with dba.peakset()
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updated 5.9 years ago by ★ 5.2k • written 5.9 years ago by • 0
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DiffBind: dealing with replicates
diffbind chipseq
updated 5.9 years ago by ★ 5.2k • written 5.9 years ago by • 0
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How to know if I should use voomWithQualityWeights() or not?
limma RNA-Seq voom voomWithQualityWeights edgeR
updated 5.9 years ago by 53k • written 5.9 years ago by ▴ 10
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How to get list of all GOIDs with all genes in each GO term?
go annotation
updated 5.9 years ago by 68k • written 5.9 years ago by • 0
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Trouble using affy library
software error R microarray affy
updated 5.9 years ago by 68k • written 5.9 years ago by • 0
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MEDIPS - Error in MEDIPS.CpGenrich
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updated 5.9 years ago by ▴ 570 • written 5.9 years ago by ▴ 20
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Remove batch effect for DESeq2
deseq2
updated 5.9 years ago by 68k • written 5.9 years ago by • 0
3
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Does a specific bioconductor version constrain versions of non-bioconductor packages?
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updated 5.9 years ago by ★ 6.6k • written 5.9 years ago by ▴ 40
46,730 results • Page 175 of 935
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Wilcox/Mann-Whitney-U cannot work because it is bound to sample size even when all of group X are lower than all of group Y. At 4 vs 3 the …
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I could install ChemmineOB on my MacBook Pro M1 Max using this procedure **1. Install open-babel and eigen using homebrew and create a cus…
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The design matrix that I described above is completely general. I imagine that it would be possible to use the same approach to generate fu…
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Cool, glad to hear I wasn't missing some functionality in DESeq2. I don't know that much about the differences between DESeq2 vs edgeR; my …
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Yes, so for one thing, note that Gordon has provided code for doing what you are asking in edgeR, which you can go ahead and use. You aske…
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Answer: When to use edgeR or limma
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