Showing : rnaseqgene • reset
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RNA-seq with DESeq2 shrinkage estimation
Regression DESeq2 rnaseqGene
updated 6 months ago by 68k • written 6 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 7 months ago by • 0
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3
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636
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Trouble with creating Series RNA-seq normalized counts matrix
GEO rnaseqGene RNA
7 months ago gallantk5 • 0
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Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
7 months ago JG13 • 0
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Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 8 months ago by ▴ 10 • written 9 months ago by • 0
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Deseq2
DESeq2 rnaseqGene
updated 8 months ago by ▴ 220 • written 8 months ago by • 0
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 9 months ago by ★ 4.7k • written 9 months ago by • 0
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
9 months ago sajadahmad41454 • 0
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 11 months ago by 52k • written 11 months ago by • 0
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DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 11 months ago by 43k • written 12 months ago by ▴ 10
2
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513
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Continuous variable to identify responder genes using DESeq2
DESeq2 rnaseqGene DifferentialExpression
updated 12 months ago by 43k • written 12 months ago by ▴ 20
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Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
13 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 15 months ago by 43k • written 15 months ago by ▴ 60
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R could not could not find function "makeTxDbFromGFF" after loading (GenomicFeatures)
rnaseqGene
updated 19 months ago by 43k • written 19 months ago by • 0
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1.2k
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Bulk RNA seq with deseq2, rnaseqGene, or edgeR
DESeq2 edgeR rnaseqGene
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
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Gene ontology enrichment analysis
rnaseq rnaseqGene geneontology
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
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1.2k
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toptable sort .by set
limma rnaseqGene
2.8 years ago snowmattin • 0
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1.1k
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Ensembl dataset version
tximport rna rnaseqGene biomaRt
updated 3.1 years ago by ★ 4.7k • written 3.1 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 3.3 years ago by 43k • written 3.3 years ago by ▴ 20
4
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1
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2.7k
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mitochondrial RNA percentage in bulk RNAseq data
rnaseqGene RNASeqR DESeq2 RNAseq
updated 3.3 years ago by 43k • written 3.3 years ago by ▴ 10
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Deseq2 Resul variation by LFC variation
rnaseqGene DESeq2 Transcriptomics
3.4 years ago • updated 21 months ago diangomaiga • 0
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DESeq2 - one groups with no replicates
DESeq2 rnaseqGene DifferentialExpression GeneExpression
3.7 years ago SUMIT • 0
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946
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display .CT files in a BioC package
RNAinteract rnaseqGene RNASeqRData rnaseqcomp
4.0 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
4.0 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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988
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typo in rnaseqGene workflow vignette.
rnaseqGene workflow deseq2
updated 5.1 years ago by 43k • written 5.1 years ago by ★ 1.5k
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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 5.7 years ago by 25k • written 5.7 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
6.0 years ago courtney.stairs • 0
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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 68k • written 6.0 years ago by ▴ 10
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5
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9.1k
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How to find Top 10 expressed genes in DESeq2
deseq2 baseMean differential gene expression rnaseqgene
updated 6.1 years ago by ★ 1.4k • written 6.1 years ago by • 0
1
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3
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1.6k
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how to find expressed genes in RNAseq
deseq2 rnaseq differential gene expression featurecounts rnaseqGene
6.2 years ago • updated 6.1 years ago melkile26 • 0
2
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5
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1.9k
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Accessing R 3.4.2 version on mac, to use 'rnaseqGene' package
rnaseq rnaseqgene R 3.4.2 Mac
updated 6.9 years ago by 4.1k • written 6.9 years ago by • 0
0
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2
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1.6k
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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 8.7 years ago by ★ 6.8k • written 8.7 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 8.7 years ago by • 0 • written 8.7 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
8.9 years ago cirisarri95 • 0
0
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1
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2.2k
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Unable to access index for repository... rnaseqGene sequencing workflows
rnaseqGene genomic sequencing
updated 9.3 years ago by ★ 8.2k • written 9.3 years ago by • 0
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6
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4.3k
views
Problem when constructing a TxDb with makeTxDbFromGFF:Error in dbGetQuery(conn,SQL) :
R differential expression rnaseqgene
9.4 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 9.6 years ago by 68k • written 9.6 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 9.7 years ago by ★ 8.2k • written 9.7 years ago by • 0
0
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2
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3.4k
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Using RNA-Seq Workflow using Real Life FASTQ data - and Mouse Reference Genome
deseq2 deseqdataset rnaseqgene fastq reference genome
updated 9.8 years ago by 68k • written 9.8 years ago by • 0
0
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2
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6.0k
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Plots and Heat Maps not displaying in RGui Window
plot heatmap graphical rnaseqgene deseqdataset
9.8 years ago greg.mulhearn • 0
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3
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2.0k
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Questions regarding convertIDs in the rnaseqGene Package
rnaseqGene convertIDs
9.9 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
10.0 years ago snf ▴ 10
44 results • Page 1 of 1
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Comment: Differential variance analysis - can i use deseq2 by Michael Love 43k
VST is valid for working with expression data on a variance stabilized scale, so yes. There are many papers that have used VST and then com…
Answer: Use of limma R package with targeted proteomics for DE analysis by Gordon Smyth 52k
It is usual to analyse log normalized values from Olink in limma. Just a straight log transformation should be sufficient. We find that `tr…
Comment: WGCNA by pammelala304 • 0
Thank you for your time and effort. I am so grateful! Play game [block blast](https://blockblastpuzzle.io) free.
Comment: Does anyone have the command to download all of the core_nt using blast_db_get() by Matthew Thornton ▴ 380
Ok. So I guess the core_nt is over 300Gb compressed. I can do it, but maybe it is better to just use ncbi-tools over the internet and just…
Comment: normalizatino of dna methylation EPIC data by user_bioinfo • 0
yes actually that's why I did, and its all good! thank you for your response
Votes
Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
Answer: normalizatino of dna methylation EPIC data
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Suggesting changing the "reply-to" field to the mailing list address.
Answer: UniProt.ws query for single UniRef90 ID takes several minutes
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