Showing : rnaseqgene • reset
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RNA-seq with DESeq2 shrinkage estimation
Regression DESeq2 rnaseqGene
updated 3 months ago by 67k • written 3 months ago by • 0
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6
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A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 4 months ago by • 0
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3
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539
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Trouble with creating Series RNA-seq normalized counts matrix
GEO rnaseqGene RNA
4 months ago gallantk5 • 0
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Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
5 months ago JG13 • 0
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Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 6 months ago by ▴ 10 • written 6 months ago by • 0
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Deseq2
DESeq2 rnaseqGene
updated 6 months ago by ▴ 220 • written 6 months ago by • 0
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 6 months ago by ★ 4.6k • written 6 months ago by • 0
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
6 months ago sajadahmad41454 • 0
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 8 months ago by 52k • written 8 months ago by • 0
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DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 9 months ago by 43k • written 9 months ago by ▴ 10
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Continuous variable to identify responder genes using DESeq2
DESeq2 rnaseqGene DifferentialExpression
updated 10 months ago by 43k • written 10 months ago by ▴ 20
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Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
10 months ago Shaimaa Gamal • 0
1
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rnaSeqGene workflow not available in Bioconductor 3.18
rnaseqGene Bioconductor3.18 DifferentialExpression release
updated 13 months ago by 43k • written 13 months ago by ▴ 60
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R could not could not find function "makeTxDbFromGFF" after loading (GenomicFeatures)
rnaseqGene
updated 16 months ago by 43k • written 16 months ago by • 0
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3
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1.1k
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Bulk RNA seq with deseq2, rnaseqGene, or edgeR
DESeq2 edgeR rnaseqGene
updated 23 months ago by 43k • written 23 months ago by • 0
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Gene ontology enrichment analysis
rnaseq rnaseqGene geneontology
updated 2.0 years ago by 67k • written 2.0 years ago by • 0
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toptable sort .by set
limma rnaseqGene
2.6 years ago snowmattin • 0
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1.1k
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Ensembl dataset version
tximport rna rnaseqGene biomaRt
updated 2.9 years ago by ★ 4.6k • written 2.9 years ago by • 0
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10
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rnaseqGene: Different output when generating step by step airway dataset
tximeta DESeq2 rnaseqGene
updated 3.1 years ago by 43k • written 3.1 years ago by ▴ 20
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2.5k
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mitochondrial RNA percentage in bulk RNAseq data
rnaseqGene RNASeqR DESeq2 RNAseq
updated 3.1 years ago by 43k • written 3.1 years ago by ▴ 10
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Deseq2 Resul variation by LFC variation
rnaseqGene DESeq2 Transcriptomics
3.1 years ago • updated 18 months ago diangomaiga • 0
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DESeq2 - one groups with no replicates
DESeq2 rnaseqGene DifferentialExpression GeneExpression
3.5 years ago SUMIT • 0
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908
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display .CT files in a BioC package
RNAinteract rnaseqGene RNASeqRData rnaseqcomp
3.8 years ago Bogdan ▴ 670
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1.6k
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Contamination in bulkseq samples. Looking at correlated genes?
RNASeqData DESeq2 rnaseqGene
3.8 years ago Seaweed • 0
3
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3
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1.1k
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A problem about RNA-seq workflow:9 Time course experiments
rnaseqgene
updated 4.5 years ago by 43k • written 4.5 years ago by ▴ 40
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3
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938
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typo in rnaseqGene workflow vignette.
rnaseqGene workflow deseq2
updated 4.9 years ago by 43k • written 4.9 years ago by ★ 1.5k
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7
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3.3k
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Issue installing RNA-seq workflow
software error deseq2 workflow rnaseqGene
updated 5.5 years ago by 25k • written 5.5 years ago by • 0
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2
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1.1k
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DESEQ2: rnaseqGene fisison tutorial time course graph has non-numerical x-axis
deseq2 rnaseqGene
5.7 years ago courtney.stairs • 0
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1.4k
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how to install package of "rnaseqGene" for R (ver: 3.5.2) for windows
rnaseqGene
updated 5.8 years ago by 67k • written 5.8 years ago by ▴ 10
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5
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How to find Top 10 expressed genes in DESeq2
deseq2 baseMean differential gene expression rnaseqgene
updated 5.8 years ago by ★ 1.4k • written 5.8 years ago by • 0
1
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3
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1.5k
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how to find expressed genes in RNAseq
deseq2 rnaseq differential gene expression featurecounts rnaseqGene
6.0 years ago • updated 5.9 years ago melkile26 • 0
2
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5
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1.9k
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Accessing R 3.4.2 version on mac, to use 'rnaseqGene' package
rnaseq rnaseqgene R 3.4.2 Mac
updated 6.6 years ago by 4.1k • written 6.6 years ago by • 0
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1.5k
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Is there a data package containing complex RNA-Seq data?
RNAseqdataset airway deseq2 rangedsummarizedexperiment rnaseqgene
updated 6.7 years ago by ▴ 160 • written 6.7 years ago by • 0
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1
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1.9k
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can't install workflow "rnaseqGene" with Bioconductor version3.3
bioconductor workflowinstall error rnaseqgene
updated 8.5 years ago by ★ 6.8k • written 8.5 years ago by ▴ 20
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4
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2.0k
views
workflow.R in BioC 3.3
workflows rnaseqgene
updated 8.5 years ago by • 0 • written 8.5 years ago by • 0
2
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5
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3.3k
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Programs used in RNA-seq workflow
deseq2 bioconductor workflows differential gene expression rnaseqgene
8.7 years ago cirisarri95 • 0
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2.2k
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Unable to access index for repository... rnaseqGene sequencing workflows
rnaseqGene genomic sequencing
updated 9.1 years ago by ★ 8.2k • written 9.1 years ago by • 0
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6
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4.2k
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Problem when constructing a TxDb with makeTxDbFromGFF:Error in dbGetQuery(conn,SQL) :
R differential expression rnaseqgene
9.1 years ago JunLVI ▴ 40
3
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2
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1.9k
views
Annotating RNAseq with GO (gene ontology) returns #NA for (nearly) all Entrez ids.
org.mm.eg.db annotation rnaseqgene
updated 9.4 years ago by 67k • written 9.4 years ago by • 0
6
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8
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2.7k
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error in RNA-Seq workflow at the gene level
rnaseqgene genomicalignments
updated 9.5 years ago by ★ 8.2k • written 9.5 years ago by • 0
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2
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3.3k
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Using RNA-Seq Workflow using Real Life FASTQ data - and Mouse Reference Genome
deseq2 deseqdataset rnaseqgene fastq reference genome
updated 9.6 years ago by 67k • written 9.6 years ago by • 0
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2
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5.8k
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Plots and Heat Maps not displaying in RGui Window
plot heatmap graphical rnaseqgene deseqdataset
9.6 years ago greg.mulhearn • 0
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3
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1.9k
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Questions regarding convertIDs in the rnaseqGene Package
rnaseqGene convertIDs
9.7 years ago Cheng-Yuan Kao ▴ 100
0
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0
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1.4k
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Minor error in the RNASeqGene workflow
rnaseqgene
9.8 years ago snf ▴ 10
44 results • Page 1 of 1
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Answer: scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data by Aaron Lun ★ 28k
You don't mention how your matrix data is being represented, but if it's a file-backed matrix (e.g., `HDF5Matrix` or one of its variants, b…
Comment: contrast matrix design for a continuous variable by dtzhu337 • 0
Thank you, Gordon. X is time splines for time point, and yes, it's needed. However, I was also thinking to incorporate time point with se…
Answer: contrast matrix design for a continuous variable by Gordon Smyth 52k
Yes, the design and contrasts are correct. Your analysis is also adjusted for covariates defined by X, which I assume is what you want to …
Comment: fail to use addPerROIQC in Rmd by liu.n • 0
That's odd. So it can run successfully within markdown but would be failed when knitting?
Comment: fail to use addPerROIQC in Rmd by joseph.joonsang • 0
> dim(spe) [1] 19962 425
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Answer: contrast matrix design for a continuous variable
A: What's the difference between p.adjust and qvalue?
Answer: DESeq2- merging technical vs biological replicates
Comment: What type of counts data to import for performing Isoform analysis in edgeR
Answer: What type of counts data to import for performing Isoform analysis in edgeR
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