Showing : rnaseqgene • reset
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Interaction in Design Experimental
rnaseqGene
6 months ago Ferdinand David • 0
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4
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Heatmap of the Count Matrix
rnaseqGene
updated 12 weeks ago by • 0 • written 6 months ago by • 0
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1
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855
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Workflow to Analyse DNA Sequence specify gene expression in a fungus under stress
rnaseqGene
updated 6 months ago by 43k • written 6 months ago by • 0
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3
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908
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RNA-seq with DESeq2 shrinkage estimation
Regression DESeq2 rnaseqGene
updated 16 months ago by 68k • written 16 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 16 months ago by • 0
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3
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946
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Trouble with creating Series RNA-seq normalized counts matrix
GEO rnaseqGene RNA
16 months ago gallantk5 • 0
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720
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Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
17 months ago JG13 • 0
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2
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896
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Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 18 months ago by ▴ 10 • written 18 months ago by • 0
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2
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Deseq2
DESeq2 rnaseqGene
updated 18 months ago by ▴ 220 • written 18 months ago by • 0
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1
reply
725
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 19 months ago by ★ 5.0k • written 19 months ago by • 0
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7
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2.0k
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
19 months ago sajadahmad41454 • 0
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2
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 21 months ago by 53k • written 21 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 21 months ago by 43k • written 21 months ago by ▴ 10
2
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1
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764
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Continuous variable to identify responder genes using DESeq2
DESeq2 rnaseqGene DifferentialExpression
updated 22 months ago by 43k • written 22 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
22 months ago Shaimaa Gamal • 0
1
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4
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1.2k
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rnaSeqGene workflow not available in Bioconductor 3.18
rnaseqGene Bioconductor3.18 DifferentialExpression release
updated 2.1 years ago by 43k • written 2.1 years ago by ▴ 60
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2.2k
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R could not could not find function "makeTxDbFromGFF" after loading (GenomicFeatures)
rnaseqGene
updated 2.4 years ago by 43k • written 2.4 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 2.9 years ago by 43k • written 2.9 years ago by • 0
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3
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3.2k
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Gene ontology enrichment analysis
rnaseq rnaseqGene geneontology
updated 3.1 years ago by 68k • written 3.1 years ago by • 0
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1.5k
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toptable sort .by set
limma rnaseqGene
3.6 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 3.9 years ago by ★ 5.0k • written 3.9 years ago by • 0
6
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10
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2.4k
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rnaseqGene: Different output when generating step by step airway dataset
tximeta DESeq2 rnaseqGene
updated 4.1 years ago by 43k • written 4.1 years ago by ▴ 20
4
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1
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3.1k
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mitochondrial RNA percentage in bulk RNAseq data
rnaseqGene RNASeqR DESeq2 RNAseq
updated 4.1 years ago by 43k • written 4.1 years ago by ▴ 10
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2
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1.3k
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Deseq2 Resul variation by LFC variation
rnaseqGene DESeq2 Transcriptomics
4.2 years ago • updated 2.6 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
4.5 years ago SUMIT • 0
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0
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1.1k
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display .CT files in a BioC package
RNAinteract rnaseqGene RNASeqRData rnaseqcomp
4.8 years ago Bogdan ▴ 670
1
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6
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2.0k
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Contamination in bulkseq samples. Looking at correlated genes?
RNASeqData DESeq2 rnaseqGene
4.8 years ago Seaweed • 0
3
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3
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1.3k
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A problem about RNA-seq workflow:9 Time course experiments
rnaseqgene
updated 5.5 years ago by 43k • written 5.5 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 5.9 years ago by 43k • written 5.9 years ago by ★ 1.5k
0
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7
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3.8k
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Issue installing RNA-seq workflow
software error deseq2 workflow rnaseqGene
updated 6.5 years ago by 25k • written 6.5 years ago by • 0
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2
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1.4k
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DESEQ2: rnaseqGene fisison tutorial time course graph has non-numerical x-axis
deseq2 rnaseqGene
6.8 years ago courtney.stairs • 0
1
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2
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1.6k
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how to install package of "rnaseqGene" for R (ver: 3.5.2) for windows
rnaseqGene
updated 6.8 years ago by 68k • written 6.8 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 6.8 years ago by ★ 1.4k • written 6.8 years ago by • 0
1
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3
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1.8k
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how to find expressed genes in RNAseq
deseq2 rnaseq differential gene expression featurecounts rnaseqGene
7.0 years ago • updated 6.9 years ago melkile26 • 0
2
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5
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2.2k
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Accessing R 3.4.2 version on mac, to use 'rnaseqGene' package
rnaseq rnaseqgene R 3.4.2 Mac
updated 7.6 years ago by 4.2k • written 7.6 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 7.7 years ago by ▴ 160 • written 7.7 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 9.5 years ago by ★ 6.8k • written 9.5 years ago by ▴ 20
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4
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2.4k
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workflow.R in BioC 3.3
workflows rnaseqgene
updated 9.5 years ago by • 0 • written 9.5 years ago by • 0
2
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5
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3.6k
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Programs used in RNA-seq workflow
deseq2 bioconductor workflows differential gene expression rnaseqgene
9.7 years ago cirisarri95 • 0
0
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1
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2.4k
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Unable to access index for repository... rnaseqGene sequencing workflows
rnaseqGene genomic sequencing
updated 10.1 years ago by ★ 8.2k • written 10.1 years ago by • 0
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
10.2 years ago • updated 10.1 years ago JunLVI ▴ 40
3
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2
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2.2k
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Annotating RNAseq with GO (gene ontology) returns #NA for (nearly) all Entrez ids.
org.mm.eg.db annotation rnaseqgene
updated 10.4 years ago by 68k • written 10.4 years ago by • 0
6
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8
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3.0k
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error in RNA-Seq workflow at the gene level
rnaseqgene genomicalignments
updated 10.5 years ago by ★ 8.2k • written 10.5 years ago by • 0
0
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2
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3.7k
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Using RNA-Seq Workflow using Real Life FASTQ data - and Mouse Reference Genome
deseq2 deseqdataset rnaseqgene fastq reference genome
updated 10.6 years ago by 68k • written 10.6 years ago by • 0
0
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2
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6.7k
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Plots and Heat Maps not displaying in RGui Window
plot heatmap graphical rnaseqgene deseqdataset
10.6 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
10.7 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
10.8 years ago snf ▴ 10
47 results • Page 1 of 1
Recent ...
Replies
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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