Showing : rnaseqgene • reset
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RNA-seq with DESeq2 shrinkage estimation
Regression DESeq2 rnaseqGene
updated 8 months ago by 68k • written 8 months ago by • 0
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A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 9 months ago by • 0
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Trouble with creating Series RNA-seq normalized counts matrix
GEO rnaseqGene RNA
9 months ago gallantk5 • 0
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Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
10 months ago JG13 • 0
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Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 10 months ago by ▴ 10 • written 11 months ago by • 0
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Deseq2
DESeq2 rnaseqGene
updated 11 months ago by ▴ 220 • written 11 months ago by • 0
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 11 months ago by ★ 4.8k • written 11 months ago by • 0
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
11 months ago sajadahmad41454 • 0
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 13 months ago by 52k • written 13 months ago by • 0
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DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 13 months ago by 43k • written 14 months ago by ▴ 10
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Continuous variable to identify responder genes using DESeq2
DESeq2 rnaseqGene DifferentialExpression
updated 14 months ago by 43k • written 14 months ago by ▴ 20
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Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
15 months ago Shaimaa Gamal • 0
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rnaSeqGene workflow not available in Bioconductor 3.18
rnaseqGene Bioconductor3.18 DifferentialExpression release
updated 17 months ago by 43k • written 17 months ago by ▴ 60
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R could not could not find function "makeTxDbFromGFF" after loading (GenomicFeatures)
rnaseqGene
updated 21 months ago by 43k • written 21 months ago by • 0
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Bulk RNA seq with deseq2, rnaseqGene, or edgeR
DESeq2 edgeR rnaseqGene
updated 2.3 years ago by 43k • written 2.3 years ago by • 0
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Gene ontology enrichment analysis
rnaseq rnaseqGene geneontology
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
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toptable sort .by set
limma rnaseqGene
3.0 years ago snowmattin • 0
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Ensembl dataset version
tximport rna rnaseqGene biomaRt
updated 3.3 years ago by ★ 4.8k • written 3.3 years ago by • 0
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rnaseqGene: Different output when generating step by step airway dataset
tximeta DESeq2 rnaseqGene
updated 3.5 years ago by 43k • written 3.5 years ago by ▴ 20
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mitochondrial RNA percentage in bulk RNAseq data
rnaseqGene RNASeqR DESeq2 RNAseq
updated 3.5 years ago by 43k • written 3.5 years ago by ▴ 10
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Deseq2 Resul variation by LFC variation
rnaseqGene DESeq2 Transcriptomics
3.5 years ago • updated 23 months ago diangomaiga • 0
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DESeq2 - one groups with no replicates
DESeq2 rnaseqGene DifferentialExpression GeneExpression
3.9 years ago SUMIT • 0
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display .CT files in a BioC package
RNAinteract rnaseqGene RNASeqRData rnaseqcomp
4.2 years ago Bogdan ▴ 670
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Contamination in bulkseq samples. Looking at correlated genes?
RNASeqData DESeq2 rnaseqGene
4.2 years ago Seaweed • 0
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1.2k
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A problem about RNA-seq workflow:9 Time course experiments
rnaseqgene
updated 4.9 years ago by 43k • written 4.9 years ago by ▴ 40
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typo in rnaseqGene workflow vignette.
rnaseqGene workflow deseq2
updated 5.3 years ago by 43k • written 5.3 years ago by ★ 1.5k
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Issue installing RNA-seq workflow
software error deseq2 workflow rnaseqGene
updated 5.8 years ago by 25k • written 5.8 years ago by • 0
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DESEQ2: rnaseqGene fisison tutorial time course graph has non-numerical x-axis
deseq2 rnaseqGene
6.1 years ago courtney.stairs • 0
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how to install package of "rnaseqGene" for R (ver: 3.5.2) for windows
rnaseqGene
updated 6.2 years ago by 68k • written 6.2 years ago by ▴ 10
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How to find Top 10 expressed genes in DESeq2
deseq2 baseMean differential gene expression rnaseqgene
updated 6.2 years ago by ★ 1.4k • written 6.2 years ago by • 0
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how to find expressed genes in RNAseq
deseq2 rnaseq differential gene expression featurecounts rnaseqGene
6.4 years ago • updated 6.3 years ago melkile26 • 0
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Accessing R 3.4.2 version on mac, to use 'rnaseqGene' package
rnaseq rnaseqgene R 3.4.2 Mac
updated 7.0 years ago by 4.1k • written 7.0 years ago by • 0
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Is there a data package containing complex RNA-Seq data?
RNAseqdataset airway deseq2 rangedsummarizedexperiment rnaseqgene
updated 7.1 years ago by ▴ 160 • written 7.1 years ago by • 0
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2.0k
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can't install workflow "rnaseqGene" with Bioconductor version3.3
bioconductor workflowinstall error rnaseqgene
updated 8.9 years ago by ★ 6.8k • written 8.9 years ago by ▴ 20
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workflow.R in BioC 3.3
workflows rnaseqgene
updated 8.9 years ago by • 0 • written 8.9 years ago by • 0
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3.4k
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Programs used in RNA-seq workflow
deseq2 bioconductor workflows differential gene expression rnaseqgene
9.1 years ago cirisarri95 • 0
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2.3k
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Unable to access index for repository... rnaseqGene sequencing workflows
rnaseqGene genomic sequencing
updated 9.5 years ago by ★ 8.2k • written 9.5 years ago by • 0
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Problem when constructing a TxDb with makeTxDbFromGFF:Error in dbGetQuery(conn,SQL) :
R differential expression rnaseqgene
9.5 years ago JunLVI ▴ 40
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Annotating RNAseq with GO (gene ontology) returns #NA for (nearly) all Entrez ids.
org.mm.eg.db annotation rnaseqgene
updated 9.8 years ago by 68k • written 9.8 years ago by • 0
6
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error in RNA-Seq workflow at the gene level
rnaseqgene genomicalignments
updated 9.9 years ago by ★ 8.2k • written 9.9 years ago by • 0
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3.5k
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Using RNA-Seq Workflow using Real Life FASTQ data - and Mouse Reference Genome
deseq2 deseqdataset rnaseqgene fastq reference genome
updated 10.0 years ago by 68k • written 10.0 years ago by • 0
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Plots and Heat Maps not displaying in RGui Window
plot heatmap graphical rnaseqgene deseqdataset
10.0 years ago greg.mulhearn • 0
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Questions regarding convertIDs in the rnaseqGene Package
rnaseqGene convertIDs
10.1 years ago Cheng-Yuan Kao ▴ 100
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1.5k
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Minor error in the RNASeqGene workflow
rnaseqgene
10.2 years ago snf ▴ 10
44 results • Page 1 of 1
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Comment: GSEA preranked analysis downstream of DEseq2 by Ajay • 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file by janwilseo • 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis by donnycrimson • 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender by donnycrimson • 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Votes
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
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