Showing : rnaseqgene • reset
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RNA-seq with DESeq2 shrinkage estimation
Regression DESeq2 rnaseqGene
updated 4 months ago by 67k • written 5 months ago by • 0
3
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6
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840
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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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575
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Trouble with creating Series RNA-seq normalized counts matrix
GEO rnaseqGene RNA
5 months ago gallantk5 • 0
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361
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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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558
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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 7 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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410
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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 • updated 7 months ago sajadahmad41454 • 0
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2
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592
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 9 months ago by 52k • written 9 months ago by • 0
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5
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DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 10 months ago by 43k • written 10 months ago by ▴ 10
2
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1
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465
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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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1.0k
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Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
11 months ago Shaimaa Gamal • 0
1
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4
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855
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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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3
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1.1k
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Bulk RNA seq with deseq2, rnaseqGene, or edgeR
DESeq2 edgeR rnaseqGene
updated 24 months 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 2.1 years ago by 67k • written 2.1 years ago by • 0
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2
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1.2k
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toptable sort .by set
limma rnaseqGene
2.7 years ago • updated 2.6 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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2
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1.1k
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Deseq2 Resul variation by LFC variation
rnaseqGene DESeq2 Transcriptomics
3.2 years ago • updated 19 months ago diangomaiga • 0
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2.0k
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DESeq2 - one groups with no replicates
DESeq2 rnaseqGene DifferentialExpression GeneExpression
3.6 years ago SUMIT • 0
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0
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924
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display .CT files in a BioC package
RNAinteract rnaseqGene RNASeqRData rnaseqcomp
3.9 years ago Bogdan ▴ 670
1
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6
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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
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A problem about RNA-seq workflow:9 Time course experiments
rnaseqgene
updated 4.6 years ago by 43k • written 4.6 years ago by ▴ 40
1
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3
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953
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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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3.3k
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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
5.8 years ago courtney.stairs • 0
1
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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 5.9 years ago by 67k • written 5.9 years ago by ▴ 10
3
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5
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8.8k
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How to find Top 10 expressed genes in DESeq2
deseq2 baseMean differential gene expression rnaseqgene
updated 5.9 years ago by ★ 1.4k • written 5.9 years ago by • 0
1
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3
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1.5k
views
how to find expressed genes in RNAseq
deseq2 rnaseq differential gene expression featurecounts rnaseqGene
6.0 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 6.7 years ago by 4.1k • written 6.7 years ago by • 0
0
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2
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1.5k
views
Is there a data package containing complex RNA-Seq data?
RNAseqdataset airway deseq2 rangedsummarizedexperiment rnaseqgene
updated 6.8 years ago by ▴ 160 • written 6.8 years ago by • 0
0
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1
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1.9k
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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2.0k
views
workflow.R in BioC 3.3
workflows rnaseqgene
updated 8.6 years ago by • 0 • written 8.6 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
9.2 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
9.7 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
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Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Gordon Smyth 52k
Sorry, I had forgotten estimateGLMDisp() produces weights as well as NB dispersions. The weights from estimatGLMRobustDisp() were intended …
Answer: Mean variance curve troubleshoot filtering by Gordon Smyth 52k
You could use `filterByExpr()`, as recommended by Law et al (2018) and in the limma and edgeR case studies. However, the main problem wi…
Comment: How do I fix an odd voom plot in a combined dataset? by Gordon Smyth 52k
The fact that you have partial NA coefficients indicates that your merged dataset consists in good part of NAs for a very large number of g…
Comment: How do I fix an odd voom plot in a combined dataset? by 1sunmic2 • 0
Thanks for responding! I did change the code slightly: dge1 <- DGEList(counts = combined_data_counts) keep <- rowSums(cpm(dge1)…
Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Andre • 0
The estimateGLMRobustDisp() function seems to have an effect on glmQLFit(), even in edgeR 4 (4.4.1). If I use estimateGLMRobustDisp(), like…
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Answer: How do I fix an odd voom plot in a combined dataset?
Answer: How do I fix an odd voom plot in a combined dataset?
Comment: How do I fix an odd voom plot in a combined dataset?
C: How does edgeR cpm function calculate log(CPM) values?
C: How does edgeR cpm function calculate log(CPM) values?
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