Showing : rnaseqgene • reset
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RNA-seq with DESeq2 shrinkage estimation
Regression DESeq2 rnaseqGene
updated 3 months ago by 67k • written 3 months ago by • 0
3
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6
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771
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A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 3 months ago by • 0
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3
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511
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Trouble with creating Series RNA-seq normalized counts matrix
GEO rnaseqGene RNA
3 months ago gallantk5 • 0
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289
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Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
4 months ago JG13 • 0
2
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2
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490
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Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 5 months ago by ▴ 10 • written 5 months ago by • 0
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445
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Deseq2
DESeq2 rnaseqGene
updated 5 months ago by ▴ 210 • written 5 months ago by • 0
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1
reply
344
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 6 months ago by ★ 4.5k • written 6 months ago by • 0
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7
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1.0k
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
6 months ago sajadahmad41454 • 0
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2
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550
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 7 months ago by 51k • written 7 months ago by • 0
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5
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1.0k
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DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 8 months ago by 42k • written 8 months ago by ▴ 10
2
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1
reply
425
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Continuous variable to identify responder genes using DESeq2
DESeq2 rnaseqGene DifferentialExpression
updated 9 months ago by 42k • written 9 months ago by ▴ 20
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6
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934
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Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
9 months ago Shaimaa Gamal • 0
1
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4
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818
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rnaSeqGene workflow not available in Bioconductor 3.18
rnaseqGene Bioconductor3.18 DifferentialExpression release
updated 12 months ago by 42k • written 12 months ago by ▴ 60
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1.4k
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R could not could not find function "makeTxDbFromGFF" after loading (GenomicFeatures)
rnaseqGene
updated 16 months ago by 42k • written 16 months ago by • 0
1
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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 22 months ago by 42k • written 22 months ago by • 0
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2.2k
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Gene ontology enrichment analysis
rnaseq rnaseqGene geneontology
updated 24 months ago by 67k • written 24 months ago by • 0
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2
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1.1k
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toptable sort .by set
limma rnaseqGene
2.5 years ago snowmattin • 0
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1
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1.0k
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Ensembl dataset version
tximport rna rnaseqGene biomaRt
updated 2.8 years ago by ★ 4.5k • written 2.8 years ago by • 0
6
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10
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1.7k
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rnaseqGene: Different output when generating step by step airway dataset
tximeta DESeq2 rnaseqGene
updated 3.0 years ago by 42k • written 3.0 years ago by ▴ 20
4
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1
reply
2.4k
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mitochondrial RNA percentage in bulk RNAseq data
rnaseqGene RNASeqR DESeq2 RNAseq
updated 3.0 years ago by 42k • written 3.0 years ago by ▴ 10
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2
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1.0k
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Deseq2 Resul variation by LFC variation
rnaseqGene DESeq2 Transcriptomics
3.1 years ago • updated 17 months ago diangomaiga • 0
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2
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1.9k
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DESeq2 - one groups with no replicates
DESeq2 rnaseqGene DifferentialExpression GeneExpression
3.4 years ago SUMIT • 0
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0
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889
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display .CT files in a BioC package
RNAinteract rnaseqGene RNASeqRData rnaseqcomp
3.7 years ago Bogdan ▴ 670
1
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1.6k
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Contamination in bulkseq samples. Looking at correlated genes?
RNASeqData DESeq2 rnaseqGene
3.7 years ago Seaweed • 0
3
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3
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1.0k
views
A problem about RNA-seq workflow:9 Time course experiments
rnaseqgene
updated 4.5 years ago by 42k • written 4.5 years ago by ▴ 40
1
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3
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925
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typo in rnaseqGene workflow vignette.
rnaseqGene workflow deseq2
updated 4.8 years ago by 42k • written 4.8 years ago by ★ 1.5k
0
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7
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3.3k
views
Issue installing RNA-seq workflow
software error deseq2 workflow rnaseqGene
updated 5.4 years ago by 25k • written 5.4 years ago by • 0
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2
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1.1k
views
DESEQ2: rnaseqGene fisison tutorial time course graph has non-numerical x-axis
deseq2 rnaseqGene
5.7 years ago courtney.stairs • 0
1
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2
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1.4k
views
how to install package of "rnaseqGene" for R (ver: 3.5.2) for windows
rnaseqGene
updated 5.8 years ago by 67k • written 5.8 years ago by ▴ 10
3
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5
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8.6k
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How to find Top 10 expressed genes in DESeq2
deseq2 baseMean differential gene expression rnaseqgene
updated 5.8 years ago by ★ 1.4k • written 5.8 years ago by • 0
1
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3
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1.5k
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how to find expressed genes in RNAseq
deseq2 rnaseq differential gene expression featurecounts rnaseqGene
5.9 years ago melkile26 • 0
2
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5
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1.8k
views
Accessing R 3.4.2 version on mac, to use 'rnaseqGene' package
rnaseq rnaseqgene R 3.4.2 Mac
updated 6.6 years ago by 4.1k • written 6.6 years ago by • 0
0
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2
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1.5k
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Is there a data package containing complex RNA-Seq data?
RNAseqdataset airway deseq2 rangedsummarizedexperiment rnaseqgene
updated 6.7 years ago by ▴ 160 • written 6.7 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 8.4 years ago by ★ 6.8k • written 8.4 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 8.4 years ago by • 0 • written 8.5 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
8.6 years ago cirisarri95 • 0
0
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1
reply
2.2k
views
Unable to access index for repository... rnaseqGene sequencing workflows
rnaseqGene genomic sequencing
updated 9.0 years ago by ★ 8.2k • written 9.0 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
9.1 years ago JunLVI ▴ 40
3
votes
2
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1.9k
views
Annotating RNAseq with GO (gene ontology) returns #NA for (nearly) all Entrez ids.
org.mm.eg.db annotation rnaseqgene
updated 9.3 years ago by 67k • written 9.3 years ago by • 0
6
votes
8
replies
2.6k
views
error in RNA-Seq workflow at the gene level
rnaseqgene genomicalignments
updated 9.4 years ago by ★ 8.2k • written 9.4 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 9.5 years ago by 67k • written 9.5 years ago by • 0
0
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2
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5.7k
views
Plots and Heat Maps not displaying in RGui Window
plot heatmap graphical rnaseqgene deseqdataset
9.6 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
9.6 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
9.7 years ago snf ▴ 10
44 results • Page 1 of 1
Recent ...
Replies
Comment: Differential Expression Analysis with unbalanced batches without replication bet by Thili • 0
Thank you for your reply. I currently have batch-corrected data processed with scvi-tools (specifically, totalvi) and have followed the sam…
Comment: Problem at champ.load by andrew.gibbons • 0
I'd love to know if anyone has a workaround too. I've tried rolling back ChAMP and R to the previous versions that others have said work wi…
Comment: GOstats kegg analysis in wheat - help - none of the objects in the first column by GV Yoshikawa • 0
Thank you for the reply. I tried swapping columns before asking, it made no difference. head(keggframeData) path_id kegg…
Answer: Differential Expression Analysis with unbalanced batches without replication bet by Gordon Smyth 51k
> Is there an alternative model or approach in tools like edgeR, limma-voom, or DESeq2 or any other that can handle confounded batch effect…
Comment: BiomaRt Possible Ensembl SSL connectivity problems detected. by Adam • 0
I just found this workaround: httr::set_config(config(ssl_verifypeer = FALSE, ssl_verifyhost = FALSE)) at [this Stack Overflow link][…
Votes
A: Up/Down Regulated GeneList from edgeR and R
A: Up/Down Regulated GeneList from edgeR and R
A: Down/Up-regulated genes asymmetry in edgeR differential expression analysis
Answer: Combining RNAseq and microarray data using edgeR/limma-voom
Answer: How do I merge a list of GRanges?
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