Showing : rnaseqGene • reset
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Interaction in Design Experimental
rnaseqGene
7 months ago Ferdinand David • 0
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4
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Heatmap of the Count Matrix
rnaseqGene
updated 4 months ago by • 0 • written 7 months ago by • 0
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1
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908
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Workflow to Analyse DNA Sequence specify gene expression in a fungus under stress
rnaseqGene
updated 7 months ago by 43k • written 7 months ago by • 0
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3
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967
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RNA-seq with DESeq2 shrinkage estimation
Regression DESeq2 rnaseqGene
updated 17 months ago by 68k • written 17 months ago by • 0
3
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6
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1.4k
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A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 18 months ago by • 0
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3
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996
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Trouble with creating Series RNA-seq normalized counts matrix
GEO rnaseqGene RNA
18 months ago gallantk5 • 0
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782
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Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
19 months ago JG13 • 0
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2
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948
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Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 19 months ago by ▴ 10 • written 20 months ago by • 0
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2
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885
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Deseq2
DESeq2 rnaseqGene
updated 20 months ago by ▴ 220 • written 20 months ago by • 0
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1
reply
768
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 20 months ago by ★ 5.0k • written 20 months ago by • 0
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7
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2.1k
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
20 months ago sajadahmad41454 • 0
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 22 months ago by 53k • written 22 months ago by • 0
3
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5
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1.8k
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DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 22 months ago by 43k • written 23 months ago by ▴ 10
2
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1
reply
805
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Continuous variable to identify responder genes using DESeq2
DESeq2 rnaseqGene DifferentialExpression
updated 23 months ago by 43k • written 24 months ago by ▴ 20
5
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6
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1.6k
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Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
2.0 years ago Shaimaa Gamal • 0
1
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4
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1.3k
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rnaSeqGene workflow not available in Bioconductor 3.18
rnaseqGene Bioconductor3.18 DifferentialExpression release
updated 2.2 years ago by 43k • written 2.2 years ago by ▴ 60
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2.3k
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R could not could not find function "makeTxDbFromGFF" after loading (GenomicFeatures)
rnaseqGene
updated 2.5 years ago by 43k • written 2.5 years ago by • 0
1
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3
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1.5k
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Bulk RNA seq with deseq2, rnaseqGene, or edgeR
DESeq2 edgeR rnaseqGene
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
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3
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3.4k
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Gene ontology enrichment analysis
rnaseq rnaseqGene geneontology
updated 3.2 years ago by 68k • written 3.2 years ago by • 0
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toptable sort .by set
limma rnaseqGene
3.7 years ago snowmattin • 0
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1
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1.4k
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Ensembl dataset version
tximport rna rnaseqGene biomaRt
updated 4.0 years ago by ★ 5.0k • written 4.0 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 4.2 years ago by 43k • written 4.2 years ago by ▴ 20
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1
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3.2k
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mitochondrial RNA percentage in bulk RNAseq data
rnaseqGene RNASeqR DESeq2 RNAseq
updated 4.2 years ago by 43k • written 4.3 years ago by ▴ 10
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2
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1.4k
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Deseq2 Resul variation by LFC variation
rnaseqGene DESeq2 Transcriptomics
4.3 years ago • updated 2.7 years ago diangomaiga • 0
2
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2
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2.4k
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DESeq2 - one groups with no replicates
DESeq2 rnaseqGene DifferentialExpression GeneExpression
4.6 years ago SUMIT • 0
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0
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1.2k
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display .CT files in a BioC package
RNAinteract rnaseqGene RNASeqRData rnaseqcomp
4.9 years ago Bogdan ▴ 670
1
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6
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2.1k
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Contamination in bulkseq samples. Looking at correlated genes?
RNASeqData DESeq2 rnaseqGene
5.0 years ago • updated 4.9 years ago Seaweed • 0
3
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3
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1.4k
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A problem about RNA-seq workflow:9 Time course experiments
rnaseqgene
updated 5.7 years ago by 43k • written 5.7 years ago by ▴ 40
1
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3
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1.2k
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typo in rnaseqGene workflow vignette.
rnaseqGene workflow deseq2
updated 6.0 years ago by 43k • written 6.0 years ago by ★ 1.5k
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7
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3.9k
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Issue installing RNA-seq workflow
software error deseq2 workflow rnaseqGene
updated 6.6 years ago by 25k • written 6.6 years ago by • 0
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2
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DESEQ2: rnaseqGene fisison tutorial time course graph has non-numerical x-axis
deseq2 rnaseqGene
6.9 years ago courtney.stairs • 0
1
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2
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1.7k
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how to install package of "rnaseqGene" for R (ver: 3.5.2) for windows
rnaseqGene
updated 7.0 years ago by 68k • written 7.0 years ago by ▴ 10
3
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5
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10k
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How to find Top 10 expressed genes in DESeq2
deseq2 baseMean differential gene expression rnaseqgene
updated 7.0 years ago by ★ 1.4k • written 7.0 years ago by • 0
1
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3
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1.9k
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how to find expressed genes in RNAseq
deseq2 rnaseq differential gene expression featurecounts rnaseqGene
7.1 years ago melkile26 • 0
2
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5
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2.3k
views
Accessing R 3.4.2 version on mac, to use 'rnaseqGene' package
rnaseq rnaseqgene R 3.4.2 Mac
updated 7.8 years ago by 4.3k • written 7.8 years ago by • 0
0
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2
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1.8k
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Is there a data package containing complex RNA-Seq data?
RNAseqdataset airway deseq2 rangedsummarizedexperiment rnaseqgene
updated 7.9 years ago by ▴ 160 • written 7.9 years ago by • 0
0
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1
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2.1k
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can't install workflow "rnaseqGene" with Bioconductor version3.3
bioconductor workflowinstall error rnaseqgene
updated 9.6 years ago by ★ 6.8k • written 9.6 years ago by ▴ 20
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4
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2.4k
views
workflow.R in BioC 3.3
workflows rnaseqgene
updated 9.6 years ago by • 0 • written 9.7 years ago by • 0
2
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5
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3.7k
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Programs used in RNA-seq workflow
deseq2 bioconductor workflows differential gene expression rnaseqgene
9.8 years ago cirisarri95 • 0
0
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1
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2.4k
views
Unable to access index for repository... rnaseqGene sequencing workflows
rnaseqGene genomic sequencing
updated 10.2 years ago by ★ 8.2k • written 10.2 years ago by • 0
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6
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4.6k
views
Problem when constructing a TxDb with makeTxDbFromGFF:Error in dbGetQuery(conn,SQL) :
R differential expression rnaseqgene
10.3 years ago JunLVI ▴ 40
3
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2
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2.2k
views
Annotating RNAseq with GO (gene ontology) returns #NA for (nearly) all Entrez ids.
org.mm.eg.db annotation rnaseqgene
updated 10.5 years ago by 68k • written 10.5 years ago by • 0
6
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8
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3.1k
views
error in RNA-Seq workflow at the gene level
rnaseqgene genomicalignments
updated 10.6 years ago by ★ 8.2k • written 10.6 years ago by • 0
0
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2
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3.8k
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Using RNA-Seq Workflow using Real Life FASTQ data - and Mouse Reference Genome
deseq2 deseqdataset rnaseqgene fastq reference genome
updated 10.7 years ago by 68k • written 10.7 years ago by • 0
0
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2
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6.8k
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Plots and Heat Maps not displaying in RGui Window
plot heatmap graphical rnaseqgene deseqdataset
10.8 years ago greg.mulhearn • 0
0
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3
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2.2k
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Questions regarding convertIDs in the rnaseqGene Package
rnaseqGene convertIDs
10.8 years ago Cheng-Yuan Kao ▴ 100
0
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0
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1.6k
views
Minor error in the RNASeqGene workflow
rnaseqgene
10.9 years ago snf ▴ 10
47 results • Page 1 of 1
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Comment: Combining two proteomics datasets with limpa by Andrew Pattison • 0
Thanks heaps Gordon. I went with option 1 and no normalisation and all seems to have worked well. Cheers, Andrew
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
Flagging protein groups as likely contaminants in this way will be fine for a limpa analysis. The `Cont_` proteins can optionally stay in f…
Answer: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Gordon Smyth 53k
Aaron Lun was a PhD student in my Lab back in 2015, when he posted the answers about allele-specific expression that you and Mike Love have…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Michael Love 43k
You just need the mouse identifier (controls baseline) and the group specific allelic effect.
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Julia Broadbent • 0
Hi Emily, Just sharing a resource for handling contaminants - we use the methods described in [Frankenfield et al. (2022)](https://pubs.acs…
Votes
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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