Showing : rnaseqGene • reset
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RNA-seq with DESeq2 shrinkage estimation
Regression DESeq2 rnaseqGene
updated 4 months ago by 67k • written 4 months ago by • 0
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6
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819
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A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 4 months ago by • 0
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3
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557
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Trouble with creating Series RNA-seq normalized counts matrix
GEO rnaseqGene RNA
5 months ago gallantk5 • 0
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346
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Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
5 months ago JG13 • 0
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2
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535
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Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 6 months ago by ▴ 10 • written 7 months ago by • 0
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Deseq2
DESeq2 rnaseqGene
updated 6 months ago by ▴ 220 • written 6 months ago by • 0
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392
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 7 months ago by ★ 4.6k • written 7 months ago by • 0
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
7 months ago sajadahmad41454 • 0
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 9 months ago by 52k • written 9 months ago by • 0
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DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 9 months ago by 43k • written 10 months ago by ▴ 10
2
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Continuous variable to identify responder genes using DESeq2
DESeq2 rnaseqGene DifferentialExpression
updated 10 months ago by 43k • written 10 months ago by ▴ 20
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Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
11 months ago Shaimaa Gamal • 0
1
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rnaSeqGene workflow not available in Bioconductor 3.18
rnaseqGene Bioconductor3.18 DifferentialExpression release
updated 13 months ago by 43k • written 13 months ago by ▴ 60
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R could not could not find function "makeTxDbFromGFF" after loading (GenomicFeatures)
rnaseqGene
updated 17 months ago by 43k • written 17 months ago by • 0
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Bulk RNA seq with deseq2, rnaseqGene, or edgeR
DESeq2 edgeR rnaseqGene
updated 23 months ago by 43k • written 23 months ago by • 0
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Gene ontology enrichment analysis
rnaseq rnaseqGene geneontology
updated 2.1 years ago by 67k • written 2.1 years ago by • 0
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1.1k
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toptable sort .by set
limma rnaseqGene
2.6 years ago snowmattin • 0
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1
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1.1k
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Ensembl dataset version
tximport rna rnaseqGene biomaRt
updated 3.0 years ago by ★ 4.6k • written 3.0 years ago by • 0
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10
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1.8k
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rnaseqGene: Different output when generating step by step airway dataset
tximeta DESeq2 rnaseqGene
updated 3.1 years ago by 43k • written 3.1 years ago by ▴ 20
4
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1
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2.6k
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mitochondrial RNA percentage in bulk RNAseq data
rnaseqGene RNASeqR DESeq2 RNAseq
updated 3.2 years ago by 43k • written 3.2 years ago by ▴ 10
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Deseq2 Resul variation by LFC variation
rnaseqGene DESeq2 Transcriptomics
3.2 years ago • updated 19 months ago diangomaiga • 0
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DESeq2 - one groups with no replicates
DESeq2 rnaseqGene DifferentialExpression GeneExpression
3.5 years ago SUMIT • 0
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918
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display .CT files in a BioC package
RNAinteract rnaseqGene RNASeqRData rnaseqcomp
3.9 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
3.9 years ago Seaweed • 0
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3
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1.1k
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A problem about RNA-seq workflow:9 Time course experiments
rnaseqgene
updated 4.6 years ago by 43k • written 4.6 years ago by ▴ 40
1
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3
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948
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typo in rnaseqGene workflow vignette.
rnaseqGene workflow deseq2
updated 5.0 years ago by 43k • written 5.0 years ago by ★ 1.5k
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7
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3.3k
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Issue installing RNA-seq workflow
software error deseq2 workflow rnaseqGene
updated 5.5 years ago by 25k • written 5.5 years ago by • 0
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2
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1.1k
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DESEQ2: rnaseqGene fisison tutorial time course graph has non-numerical x-axis
deseq2 rnaseqGene
5.8 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 5.9 years ago by 67k • written 5.9 years ago by ▴ 10
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5
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How to find Top 10 expressed genes in DESeq2
deseq2 baseMean differential gene expression rnaseqgene
updated 5.9 years ago by ★ 1.4k • written 5.9 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
6.0 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 6.7 years ago by 4.1k • written 6.7 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 6.8 years ago by ▴ 160 • written 6.8 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 8.5 years ago by ★ 6.8k • written 8.5 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 8.6 years ago by • 0 • written 8.6 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
8.7 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 9.1 years ago by ★ 8.2k • written 9.1 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
9.2 years ago JunLVI ▴ 40
3
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2
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2.0k
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Annotating RNAseq with GO (gene ontology) returns #NA for (nearly) all Entrez ids.
org.mm.eg.db annotation rnaseqgene
updated 9.4 years ago by 67k • written 9.5 years ago by • 0
6
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8
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2.7k
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error in RNA-Seq workflow at the gene level
rnaseqgene genomicalignments
updated 9.5 years ago by ★ 8.2k • written 9.5 years ago by • 0
0
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2
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3.3k
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Using RNA-Seq Workflow using Real Life FASTQ data - and Mouse Reference Genome
deseq2 deseqdataset rnaseqgene fastq reference genome
updated 9.6 years ago by 67k • written 9.6 years ago by • 0
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2
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5.8k
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Plots and Heat Maps not displaying in RGui Window
plot heatmap graphical rnaseqgene deseqdataset
9.7 years ago greg.mulhearn • 0
0
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3
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1.9k
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Questions regarding convertIDs in the rnaseqGene Package
rnaseqGene convertIDs
9.7 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
9.8 years ago snf ▴ 10
44 results • Page 1 of 1
Recent ...
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Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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