Showing : rnaseqgene • reset
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RNA-seq with DESeq2 shrinkage estimation
Regression DESeq2 rnaseqGene
updated 9 months ago by 68k • written 9 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 9 months ago by • 0
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3
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745
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Trouble with creating Series RNA-seq normalized counts matrix
GEO rnaseqGene RNA
9 months ago gallantk5 • 0
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545
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Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
10 months ago JG13 • 0
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695
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Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 11 months ago by ▴ 10 • written 12 months ago by • 0
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Deseq2
DESeq2 rnaseqGene
updated 11 months ago by ▴ 220 • written 11 months ago by • 0
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reply
566
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 12 months ago by ★ 4.8k • written 12 months ago by • 0
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7
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
12 months ago sajadahmad41454 • 0
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 14 months ago by 52k • written 14 months ago by • 0
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5
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DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 14 months ago by 43k • written 14 months ago by ▴ 10
2
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1
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571
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Continuous variable to identify responder genes using DESeq2
DESeq2 rnaseqGene DifferentialExpression
updated 15 months ago by 43k • written 15 months ago by ▴ 20
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6
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1.2k
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Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
16 months ago • updated 15 months ago Shaimaa Gamal • 0
1
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4
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rnaSeqGene workflow not available in Bioconductor 3.18
rnaseqGene Bioconductor3.18 DifferentialExpression release
updated 18 months ago by 43k • written 18 months ago by ▴ 60
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R could not could not find function "makeTxDbFromGFF" after loading (GenomicFeatures)
rnaseqGene
updated 22 months ago by 43k • written 22 months ago by • 0
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3
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1.3k
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Bulk RNA seq with deseq2, rnaseqGene, or edgeR
DESeq2 edgeR rnaseqGene
updated 2.3 years ago by 43k • written 2.4 years ago by • 0
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3
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2.9k
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Gene ontology enrichment analysis
rnaseq rnaseqGene geneontology
updated 2.5 years ago by 68k • written 2.5 years ago by • 0
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2
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1.3k
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toptable sort .by set
limma rnaseqGene
3.0 years ago snowmattin • 0
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1
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1.2k
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Ensembl dataset version
tximport rna rnaseqGene biomaRt
updated 3.4 years ago by ★ 4.8k • written 3.4 years ago by • 0
6
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10
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rnaseqGene: Different output when generating step by step airway dataset
tximeta DESeq2 rnaseqGene
updated 3.5 years ago by 43k • written 3.5 years ago by ▴ 20
4
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1
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2.9k
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mitochondrial RNA percentage in bulk RNAseq data
rnaseqGene RNASeqR DESeq2 RNAseq
updated 3.6 years ago by 43k • written 3.6 years ago by ▴ 10
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2
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1.2k
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Deseq2 Resul variation by LFC variation
rnaseqGene DESeq2 Transcriptomics
3.6 years ago • updated 24 months ago diangomaiga • 0
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2
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2.2k
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DESeq2 - one groups with no replicates
DESeq2 rnaseqGene DifferentialExpression GeneExpression
3.9 years ago SUMIT • 0
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0
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994
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display .CT files in a BioC package
RNAinteract rnaseqGene RNASeqRData rnaseqcomp
4.3 years ago Bogdan ▴ 670
1
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6
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1.9k
views
Contamination in bulkseq samples. Looking at correlated genes?
RNASeqData DESeq2 rnaseqGene
4.3 years ago Seaweed • 0
3
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3
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1.2k
views
A problem about RNA-seq workflow:9 Time course experiments
rnaseqgene
updated 5.0 years ago by 43k • written 5.0 years ago by ▴ 40
1
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3
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1.0k
views
typo in rnaseqGene workflow vignette.
rnaseqGene workflow deseq2
updated 5.4 years ago by 43k • written 5.4 years ago by ★ 1.5k
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7
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3.6k
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Issue installing RNA-seq workflow
software error deseq2 workflow rnaseqGene
updated 5.9 years ago by 25k • written 5.9 years ago by • 0
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2
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1.2k
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DESEQ2: rnaseqGene fisison tutorial time course graph has non-numerical x-axis
deseq2 rnaseqGene
6.2 years ago courtney.stairs • 0
1
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2
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1.5k
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how to install package of "rnaseqGene" for R (ver: 3.5.2) for windows
rnaseqGene
updated 6.3 years ago by 68k • written 6.3 years ago by ▴ 10
3
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5
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9.7k
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How to find Top 10 expressed genes in DESeq2
deseq2 baseMean differential gene expression rnaseqgene
updated 6.3 years ago by ★ 1.4k • written 6.3 years ago by • 0
1
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3
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1.7k
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how to find expressed genes in RNAseq
deseq2 rnaseq differential gene expression featurecounts rnaseqGene
6.4 years ago melkile26 • 0
2
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5
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2.0k
views
Accessing R 3.4.2 version on mac, to use 'rnaseqGene' package
rnaseq rnaseqgene R 3.4.2 Mac
updated 7.1 years ago by 4.1k • written 7.1 years ago by • 0
0
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2
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1.6k
views
Is there a data package containing complex RNA-Seq data?
RNAseqdataset airway deseq2 rangedsummarizedexperiment rnaseqgene
updated 7.2 years ago by ▴ 160 • written 7.2 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 8.9 years ago by ★ 6.8k • written 8.9 years ago by ▴ 20
0
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4
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2.2k
views
workflow.R in BioC 3.3
workflows rnaseqgene
updated 9.0 years ago by • 0 • written 9.0 years ago by • 0
2
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5
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3.4k
views
Programs used in RNA-seq workflow
deseq2 bioconductor workflows differential gene expression rnaseqgene
9.1 years ago cirisarri95 • 0
0
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1
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2.3k
views
Unable to access index for repository... rnaseqGene sequencing workflows
rnaseqGene genomic sequencing
updated 9.5 years ago by ★ 8.2k • written 9.5 years ago by • 0
0
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6
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4.4k
views
Problem when constructing a TxDb with makeTxDbFromGFF:Error in dbGetQuery(conn,SQL) :
R differential expression rnaseqgene
9.6 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 9.8 years ago by 68k • written 9.9 years ago by • 0
6
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8
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2.8k
views
error in RNA-Seq workflow at the gene level
rnaseqgene genomicalignments
updated 9.9 years ago by ★ 8.2k • written 9.9 years ago by • 0
0
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2
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3.5k
views
Using RNA-Seq Workflow using Real Life FASTQ data - and Mouse Reference Genome
deseq2 deseqdataset rnaseqgene fastq reference genome
updated 10.0 years ago by 68k • written 10.0 years ago by • 0
0
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2
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6.4k
views
Plots and Heat Maps not displaying in RGui Window
plot heatmap graphical rnaseqgene deseqdataset
10.1 years ago greg.mulhearn • 0
0
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3
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2.0k
views
Questions regarding convertIDs in the rnaseqGene Package
rnaseqGene convertIDs
10.1 years ago Cheng-Yuan Kao ▴ 100
0
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0
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1.5k
views
Minor error in the RNASeqGene workflow
rnaseqgene
10.2 years ago snf ▴ 10
44 results • Page 1 of 1
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Comment: limma::voom vs edgeR::voomLmFit - when to use? by Geoff • 0
Just wondering--why was this function put into `edgeR` rather than `limma`? Maybe a bit technical, but it is a little confusing from an out…
Comment: cannot download atena annotation for human by Davide • 0
Hi Robert, I was able to solve the problem. Indeed, it stems from the co-occurrence of two different AnnotationHub available for hg38. …
Comment: Setting ylims in bam coverage plot and assigning compound sashimi numbers to ove by macdonaldfrench7286566 • 0
Regarding the ylim for the coverage [space waves][1], have you tried accessing the ylim slot of the CoverageTrack object after you've creat…
Comment: How to left_join a tidySummarizedExperiment with a GRanges object by seqnames an by Kateřina • 0
I unfortunately haven't. Non-tidy grammar is fine, but I have wanted to use tidy-only grammar. Thank you nonetheless!
Comment: GAlignments Cigar to GRanges by pineiroalejandro • 0
Wow, so easy! Thanks for your quick reply.
Votes
Answer: GAlignments Cigar to GRanges
Answer: GAlignments Cigar to GRanges
When running contrasts, does it use normalized read counts?
When running contrasts, does it use normalized read counts?
Importing Salmon counts with tximport with host and virus genomes
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