Showing : rnaseqGene • reset
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RNA-seq with DESeq2 shrinkage estimation
Regression DESeq2 rnaseqGene
updated 5 months ago by 67k • written 5 months ago by • 0
3
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6
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861
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A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 5 months ago by • 0
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3
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591
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Trouble with creating Series RNA-seq normalized counts matrix
GEO rnaseqGene RNA
6 months ago gallantk5 • 0
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379
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Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
6 months ago JG13 • 0
2
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2
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572
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Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 7 months ago by ▴ 10 • written 8 months ago by • 0
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Deseq2
DESeq2 rnaseqGene
updated 7 months ago by ▴ 220 • written 7 months ago by • 0
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reply
425
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 8 months ago by ★ 4.6k • written 8 months ago by • 0
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7
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1.2k
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
8 months ago sajadahmad41454 • 0
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598
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 10 months ago by 52k • written 10 months ago by • 0
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5
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1.2k
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DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 10 months ago by 43k • written 11 months ago by ▴ 10
2
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1
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483
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Continuous variable to identify responder genes using DESeq2
DESeq2 rnaseqGene DifferentialExpression
updated 11 months ago by 43k • written 11 months ago by ▴ 20
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6
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Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
12 months ago Shaimaa Gamal • 0
1
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4
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864
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rnaSeqGene workflow not available in Bioconductor 3.18
rnaseqGene Bioconductor3.18 DifferentialExpression release
updated 14 months ago by 43k • written 14 months ago by ▴ 60
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R could not could not find function "makeTxDbFromGFF" after loading (GenomicFeatures)
rnaseqGene
updated 18 months ago by 43k • written 18 months ago by • 0
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1.1k
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Bulk RNA seq with deseq2, rnaseqGene, or edgeR
DESeq2 edgeR rnaseqGene
updated 2.0 years ago by 43k • written 2.0 years ago by • 0
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3
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2.4k
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Gene ontology enrichment analysis
rnaseq rnaseqGene geneontology
updated 2.2 years ago by 67k • written 2.2 years ago by • 0
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1.2k
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toptable sort .by set
limma rnaseqGene
2.7 years ago snowmattin • 0
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1
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1.1k
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Ensembl dataset version
tximport rna rnaseqGene biomaRt
updated 3.0 years ago by ★ 4.6k • written 3.0 years ago by • 0
6
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10
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1.8k
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rnaseqGene: Different output when generating step by step airway dataset
tximeta DESeq2 rnaseqGene
updated 3.2 years ago by 43k • written 3.2 years ago by ▴ 20
4
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1
reply
2.6k
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mitochondrial RNA percentage in bulk RNAseq data
rnaseqGene RNASeqR DESeq2 RNAseq
updated 3.2 years ago by 43k • written 3.2 years ago by ▴ 10
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1.1k
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Deseq2 Resul variation by LFC variation
rnaseqGene DESeq2 Transcriptomics
3.3 years ago • updated 20 months ago diangomaiga • 0
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DESeq2 - one groups with no replicates
DESeq2 rnaseqGene DifferentialExpression GeneExpression
3.6 years ago SUMIT • 0
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928
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display .CT files in a BioC package
RNAinteract rnaseqGene RNASeqRData rnaseqcomp
3.9 years ago Bogdan ▴ 670
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1.7k
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Contamination in bulkseq samples. Looking at correlated genes?
RNASeqData DESeq2 rnaseqGene
3.9 years ago Seaweed • 0
3
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3
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1.1k
views
A problem about RNA-seq workflow:9 Time course experiments
rnaseqgene
updated 4.7 years ago by 43k • written 4.7 years ago by ▴ 40
1
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3
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959
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typo in rnaseqGene workflow vignette.
rnaseqGene workflow deseq2
updated 5.0 years ago by 43k • written 5.0 years ago by ★ 1.5k
0
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7
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3.4k
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Issue installing RNA-seq workflow
software error deseq2 workflow rnaseqGene
updated 5.6 years ago by 25k • written 5.6 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
5.9 years ago courtney.stairs • 0
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2
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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 6.0 years ago by 67k • written 6.0 years ago by ▴ 10
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5
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8.9k
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How to find Top 10 expressed genes in DESeq2
deseq2 baseMean differential gene expression rnaseqgene
updated 6.0 years ago by ★ 1.4k • written 6.0 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
6.1 years ago melkile26 • 0
2
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5
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1.9k
views
Accessing R 3.4.2 version on mac, to use 'rnaseqGene' package
rnaseq rnaseqgene R 3.4.2 Mac
updated 6.8 years ago by 4.1k • written 6.8 years ago by • 0
0
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2
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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 6.9 years ago by ▴ 160 • written 6.9 years ago by • 0
0
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1
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2.0k
views
can't install workflow "rnaseqGene" with Bioconductor version3.3
bioconductor workflowinstall error rnaseqgene
updated 8.6 years ago by ★ 6.8k • written 8.6 years ago by ▴ 20
0
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4
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2.1k
views
workflow.R in BioC 3.3
workflows rnaseqgene
updated 8.6 years ago by • 0 • written 8.7 years ago by • 0
2
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5
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3.3k
views
Programs used in RNA-seq workflow
deseq2 bioconductor workflows differential gene expression rnaseqgene
8.8 years ago cirisarri95 • 0
0
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1
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2.2k
views
Unable to access index for repository... rnaseqGene sequencing workflows
rnaseqGene genomic sequencing
updated 9.2 years ago by ★ 8.2k • written 9.2 years ago by • 0
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6
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4.2k
views
Problem when constructing a TxDb with makeTxDbFromGFF:Error in dbGetQuery(conn,SQL) :
R differential expression rnaseqgene
9.3 years ago JunLVI ▴ 40
3
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2
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2.0k
views
Annotating RNAseq with GO (gene ontology) returns #NA for (nearly) all Entrez ids.
org.mm.eg.db annotation rnaseqgene
updated 9.5 years ago by 67k • written 9.5 years ago by • 0
6
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8
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2.7k
views
error in RNA-Seq workflow at the gene level
rnaseqgene genomicalignments
updated 9.6 years ago by ★ 8.2k • written 9.6 years ago by • 0
0
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2
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3.3k
views
Using RNA-Seq Workflow using Real Life FASTQ data - and Mouse Reference Genome
deseq2 deseqdataset rnaseqgene fastq reference genome
updated 9.7 years ago by 67k • written 9.7 years ago by • 0
0
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2
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5.9k
views
Plots and Heat Maps not displaying in RGui Window
plot heatmap graphical rnaseqgene deseqdataset
9.8 years ago greg.mulhearn • 0
0
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3
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1.9k
views
Questions regarding convertIDs in the rnaseqGene Package
rnaseqGene convertIDs
9.8 years ago Cheng-Yuan Kao ▴ 100
0
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0
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1.4k
views
Minor error in the RNASeqGene workflow
rnaseqgene
9.9 years ago snf ▴ 10
44 results • Page 1 of 1
Recent ...
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Comment: How to sort negative log2FC or FC in RNAseq for GSEA? by QN ▴ 10
Thank you ATpoint for your response! In the result of GSEA, like you indicated, there will be gene sets that have positive NES and gene se…
Comment: EdgeR Biological CVs by ATpoint ★ 4.6k
"Joseph" is a spam bot...
Answer: How to sort negative log2FC or FC in RNAseq for GSEA? by ATpoint ★ 4.6k
GSEA asks whether there are general shifts in gene expression towards certain terms. Hence, you would not split your results tables but ord…
Comment: EdgeR Biological CVs by James • 0
Thank you Gordon and Joseph. I presume question (1) would be answered by using a prior G0 of 0? For question (2), I was expecting a biolog…
Answer: EdgeR Biological CVs by Gordon Smyth 52k
I think your questions are answered by the published paper. You might also like to consult recent papers on edgeR by Yunshun Chen and Pedro…
Votes
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
Answer: EdgeR Biological CVs
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
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