Showing : rnaseqgene • reset
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 5 weeks ago by 50k • written 5 weeks ago by • 0
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5
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DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 7 weeks ago by 41k • written 8 weeks ago by ▴ 10
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207
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Continuous variable to identify responder genes using DESeq2
DESeq2 rnaseqGene DifferentialExpression
updated 11 weeks ago by 41k • written 11 weeks ago by ▴ 20
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Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
3 months ago Shaimaa Gamal • 0
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4
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539
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rnaSeqGene workflow not available in Bioconductor 3.18
rnaseqGene Bioconductor3.18 DifferentialExpression release
updated 5 months ago by 41k • written 5 months ago by ▴ 60
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R could not could not find function "makeTxDbFromGFF" after loading (GenomicFeatures)
rnaseqGene
updated 9 months ago by 41k • written 9 months ago by • 0
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3
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Bulk RNA seq with deseq2, rnaseqGene, or edgeR
DESeq2 edgeR rnaseqGene
updated 15 months ago by 41k • written 15 months ago by • 0
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Gene ontology enrichment analysis
rnaseq rnaseqGene geneontology
updated 17 months ago by 65k • written 17 months ago by • 0
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toptable sort .by set
limma rnaseqGene
23 months ago snowmattin • 0
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Ensembl dataset version
tximport rna rnaseqGene biomaRt
updated 2.3 years ago by ★ 4.0k • written 2.3 years ago by • 0
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rnaseqGene: Different output when generating step by step airway dataset
tximeta DESeq2 rnaseqGene
updated 2.5 years ago by 41k • written 2.5 years ago by ▴ 20
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1
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1.9k
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mitochondrial RNA percentage in bulk RNAseq data
rnaseqGene RNASeqR DESeq2 RNAseq
updated 2.5 years ago by 41k • written 2.5 years ago by ▴ 10
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807
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Deseq2 Resul variation by LFC variation
rnaseqGene DESeq2 Transcriptomics
2.5 years ago • updated 11 months ago diangomaiga • 0
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DESeq2 - one groups with no replicates
DESeq2 rnaseqGene DifferentialExpression GeneExpression
2.9 years ago SUMIT • 0
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display .CT files in a BioC package
RNAinteract rnaseqGene RNASeqRData rnaseqcomp
3.2 years ago Bogdan ▴ 670
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1.3k
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Contamination in bulkseq samples. Looking at correlated genes?
RNASeqData DESeq2 rnaseqGene
3.2 years ago Seaweed • 0
3
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3
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861
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A problem about RNA-seq workflow:9 Time course experiments
rnaseqgene
updated 3.9 years ago by 41k • written 3.9 years ago by ▴ 40
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3
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756
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typo in rnaseqGene workflow vignette.
rnaseqGene workflow deseq2
updated 4.3 years ago by 41k • written 4.3 years ago by ★ 1.5k
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7
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3.0k
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Issue installing RNA-seq workflow
software error deseq2 workflow rnaseqGene
updated 4.8 years ago by 25k • written 4.8 years ago by • 0
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2
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910
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DESEQ2: rnaseqGene fisison tutorial time course graph has non-numerical x-axis
deseq2 rnaseqGene
5.1 years ago courtney.stairs • 0
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1.2k
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how to install package of "rnaseqGene" for R (ver: 3.5.2) for windows
rnaseqGene
updated 5.2 years ago by 65k • written 5.2 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 5.2 years ago by ★ 1.3k • written 5.2 years ago by • 0
1
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3
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how to find expressed genes in RNAseq
deseq2 rnaseq differential gene expression featurecounts rnaseqGene
5.4 years ago • updated 5.3 years ago melkile26 • 0
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5
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1.6k
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Accessing R 3.4.2 version on mac, to use 'rnaseqGene' package
rnaseq rnaseqgene R 3.4.2 Mac
updated 6.0 years ago by 3.8k • written 6.0 years ago by • 0
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1.3k
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Is there a data package containing complex RNA-Seq data?
RNAseqdataset airway deseq2 rangedsummarizedexperiment rnaseqgene
updated 6.1 years ago by ▴ 160 • written 6.1 years ago by • 0
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1.8k
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can't install workflow "rnaseqGene" with Bioconductor version3.3
bioconductor workflowinstall error rnaseqgene
updated 7.9 years ago by ★ 6.8k • written 7.9 years ago by ▴ 20
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4
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1.8k
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workflow.R in BioC 3.3
workflows rnaseqgene
updated 7.9 years ago by • 0 • written 7.9 years ago by • 0
2
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5
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3.0k
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Programs used in RNA-seq workflow
deseq2 bioconductor workflows differential gene expression rnaseqgene
8.1 years ago cirisarri95 • 0
0
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1
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2.0k
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Unable to access index for repository... rnaseqGene sequencing workflows
rnaseqGene genomic sequencing
updated 8.5 years ago by ★ 8.2k • written 8.5 years ago by • 0
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6
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3.9k
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Problem when constructing a TxDb with makeTxDbFromGFF:Error in dbGetQuery(conn,SQL) :
R differential expression rnaseqgene
8.5 years ago JunLVI ▴ 40
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2
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1.8k
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Annotating RNAseq with GO (gene ontology) returns #NA for (nearly) all Entrez ids.
org.mm.eg.db annotation rnaseqgene
updated 8.8 years ago by 65k • written 8.8 years ago by • 0
6
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8
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2.4k
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error in RNA-Seq workflow at the gene level
rnaseqgene genomicalignments
updated 8.9 years ago by ★ 8.2k • written 8.9 years ago by • 0
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3.0k
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Using RNA-Seq Workflow using Real Life FASTQ data - and Mouse Reference Genome
deseq2 deseqdataset rnaseqgene fastq reference genome
updated 9.0 years ago by 65k • written 9.0 years ago by • 0
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2
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5.1k
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Plots and Heat Maps not displaying in RGui Window
plot heatmap graphical rnaseqgene deseqdataset
9.0 years ago greg.mulhearn • 0
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3
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1.7k
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Questions regarding convertIDs in the rnaseqGene Package
rnaseqGene convertIDs
9.1 years ago Cheng-Yuan Kao ▴ 100
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1.2k
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Minor error in the RNASeqGene workflow
rnaseqgene
9.2 years ago snf ▴ 10
36 results • Page 1 of 1
Recent ...
Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions by JKim • 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by James W. MacDonald 65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
My code for the sessionInfo() . If the pictures are too big, I will downsize them. THank you again for reading my post ! ```r > sessionInf…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
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