Showing : rnaseqdata • reset
6
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4
replies
10k
views
How to use combat in order to remove batch effects?
BatchEffect DESeq2 RNASeqData
updated 2.3 years ago by • 0 • written 3.1 years ago by ▴ 10
3
votes
6
replies
8.7k
views
How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
DESeq2 RNASeq RNASeqData
2.1 years ago treebig44 ▴ 30
22
votes
15
replies
7.4k
views
biomaRt error unable to fix: need help troubleshooting
biomaRt RNASeqData R
updated 5 months ago by ▴ 10 • written 2.0 years ago by ▴ 50
0
votes
3
replies
7.4k
views
Package ‘#####’ was installed before R 4.0.0: please re-install it
Bioconductor RNASeqData DESeq2 Rsubread
updated 3.4 years ago by 65k • written 3.4 years ago by • 0
8
votes
2
replies
6.8k
views
handling outliers with DESeq2
RNASeqData DESeq2 Outliers
3.0 years ago paty ▴ 60
7
votes
5
replies
3.4k
views
Normalise to a housekeeping gene in DESEq2
DESeq2 housekeeping R RNASeqData
3.4 years ago ecg1g15 ▴ 20
0
votes
10
replies
2.8k
views
GenomicAlignments - Speeding up readGAlignmentPairs()
Cancer RNAseqData GenomicFeatures Cancer RNAseqData GenomicFeatures
updated 9.8 years ago by ▴ 320 • written 9.8 years ago by ★ 6.8k
2
votes
4
replies
2.8k
views
Compare 3 RNASeq groups with no control in DESeq2
anova RNASeqData tukeyTest DESeq2
3.4 years ago ecg1g15 ▴ 20
1
vote
2
replies
2.5k
views
Understanding how to contrast two treatments in DESeq2
DESeq2 RNASeqData
updated 20 months ago by ★ 1.3k • written 20 months ago by • 0
1
vote
15
replies
2.5k
views
between and within subjects design with batch correction
RNASeqData BatchEffect paired DESeq2
3.0 years ago demisa • 0
4
votes
1
reply
2.4k
views
Finding significant up-regulated and down-regulated genes given a log2FoldChange threshold
DESeq2 RNASeq RNASeqData
updated 2.1 years ago by 41k • written 2.1 years ago by ▴ 30
2
votes
8
replies
2.3k
views
While trying to remove non differentially expressed genes through limma, I am getting a warning
RNASeqData
updated 3.1 years ago by 50k • written 3.1 years ago by ▴ 20
2
votes
9
replies
2.2k
views
Stuck on how to voom-limma on RSEM data from TCGA
TCGA r RNASeqData voom limma
22 months ago Peipei • 0
0
votes
5
replies
2.2k
views
Can Differential Isoform expression analysis can be performed using DESeq2 package
RNASeqData isoform DESeq2
2.0 years ago • updated 23 months ago priyanka.m • 0
1
vote
1
reply
2.1k
views
Limma interaction term
RNASeqData limma DifferentialExpression
updated 2.1 years ago by 50k • written 2.1 years ago by • 0
1
vote
3
replies
1.7k
views
Mapping EntrezId to Ensembl IDs returns NA for pseudogenes and snoRNA
RNASeqData RNASeq RNASeqR
3.0 years ago dantasezequiel1 • 0
1
vote
7
replies
1.6k
views
DESeqDataSetFromMatrix error
BiocGenerics DESeq2 DEGreport RNASeqData DEG
updated 21 months ago by 65k • written 21 months ago by • 0
1
vote
2
replies
1.5k
views
Binning expression data along with capturing gene identifiers
rnaseqdata clustering
updated 9.3 years ago by ★ 2.0k • written 9.3 years ago by ▴ 150
1
vote
2
replies
1.4k
views
IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon IsoformSwitchAnalyzeR tximport RNASeqData
updated 8 months ago by ▴ 120 • written 9 months ago by ▴ 10
0
votes
2
replies
1.4k
views
How to run vst transformation
RNASeqData vst
updated 23 months ago by 41k • written 24 months ago by • 0
2
votes
3
replies
1.4k
views
RNA-seq analysis without replicates
DESeq2 RESEQ RNASeqData
updated 12 months ago by • 0 • written 12 months ago by • 0
3
votes
3
replies
1.4k
views
How to formulate 2 factor nested design in DESeq2
nested_design RNASeqData DESeq2
23 months ago JK Kim ▴ 20
2
votes
5
replies
1.4k
views
edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR RNASeq RNASeqData Bioconductor
written 14 months ago by • 0
1
vote
6
replies
1.3k
views
Contamination in bulkseq samples. Looking at correlated genes?
RNASeqData DESeq2 rnaseqGene
3.2 years ago Seaweed • 0
3
votes
4
replies
1.3k
views
GEO + RNA-seq. Total Newbie.
RNASeqData RNASeq GEO RNASeqR HELP
3.1 years ago hgalmoore • 0
0
votes
1
reply
1.3k
views
'Negative' and 'Positive' bigWig RNAseq files: how to deal with these???
bigWig RNASeqData
2.2 years ago bas_work ▴ 30
3
votes
6
replies
1.3k
views
Different contrast coding strategies in DESeq2 produce slightly different output?
DESeq2 RNASeqData DifferentialExpression
updated 3.4 years ago by 41k • written 3.4 years ago by ▴ 50
1
vote
4
replies
1.3k
views
Inverted Log2FC values after DEseq2 analysis
DESeq2 Log2FC RNASeqData
15 months ago Iwan • 0
2
votes
3
replies
1.2k
views
Problem with tximport IDs
tximport tx2gene rnas DESeq2 RNASeqData
24 months ago Maka • 0
1
vote
5
replies
1.2k
views
Error in DEseq
DEseq RNASeqData
updated 22 months ago by ★ 4.0k • written 22 months ago by • 0
4
votes
3
replies
1.2k
views
Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
DESeq2 idep RNASeqData
updated 2.2 years ago by ★ 1.3k • written 2.2 years ago by ▴ 10
0
votes
6
replies
1.2k
views
while doing co-expression network analysis, I am getting an error
RNASeqData
3.1 years ago • updated 3.0 years ago Rishav ▴ 20
3
votes
3
replies
1.2k
views
Differential expression analysis with only FPKM matrix available from total newbie in R
FPKM RNASeqData DEAnalysis limma
7 months ago Ethan Nguyen • 0
2
votes
4
replies
1.2k
views
DESeq2: how to integrate a manually edited matrix into full argument of DESeq
RNASeqData DESeq2
2.7 years ago khaveh ▴ 10
0
votes
2
replies
1.1k
views
lncRNA Genes in a Dataset
ncRNAtools RNASeqData
2.1 years ago sushimoto • 0
1
vote
1
reply
1.1k
views
Help understanding edgeR code for doing exactTest
exacttest RNASeqData edgeR diffGeneAnalysis
updated 2.5 years ago by 50k • written 2.5 years ago by • 0
2
votes
3
replies
1.1k
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC RNASeqData sva BatchEffect
updated 10 months ago by ★ 4.0k • written 10 months ago by ▴ 10
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 8 days ago by • 0 • written 10 months ago by • 0
0
votes
2
replies
1.1k
views
Condition shown as 'Untreated vs. Treated' in output of results() in DESeq2
RNASeqData DESeq2
updated 2.0 years ago by 41k • written 2.0 years ago by ▴ 30
1
vote
2
replies
1.1k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 11 months ago by • 0
0
votes
4
replies
1.1k
views
enhanced volcano , different -log10pvalue of the same gene
EnhancedVolcano RNASeqData DifferentialExpression
11 months ago ruba-mahmoud • 0
2
votes
3
replies
1.1k
views
bulk RNA-seq analysis using R : batch effect : One question concerning Combat-seq and one question concerning DESeq2 design = batch + condition
BatchEffect sva DESeq2 RNASeqData limma
updated 8 months ago by 65k • written 8 months ago by ▴ 10
0
votes
1
reply
1.0k
views
RNASeq analysis - Test for effect of two variables on one (Genotype)
deseq2 multiple factor design rnaseqdata
updated 8.0 years ago by 41k • written 8.0 years ago by ▴ 80
1
vote
4
replies
1.0k
views
lncRNA Differential Expression Analysis
DESeq2 limma RNASeqData
2.1 years ago sushimoto • 0
0
votes
2
replies
1.0k
views
understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData Rsubread mapping featurecounts
updated 8 months ago by 65k • written 8 months ago by • 0
0
votes
3
replies
952
views
Contrasting LogFCs in DESeq2
DESeq2 RNASeqData
updated 2.9 years ago by ★ 1.3k • written 2.9 years ago by • 0
3
votes
2
replies
931
views
DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R DEXSeq SequenceAnnotation RNASeqData
2.1 years ago • updated 24 months ago Dakarai ▴ 10
3
votes
2
replies
920
views
Why some statistically differently expressed genes are not DEGs?
RNASeqData DEGreport edgeR
3.2 years ago Wuschel ▴ 10
3
votes
3
replies
913
views
how to remove batch effects of RNA seq data based on continuous variables(like surrogate variables from sva package) using combatseq or limma (remove…
combatseq RNASeqData sva limma
10 months ago amnahsiddiqa ▴ 10
0
votes
2
replies
887
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 8 days ago by • 0 • written 17 months ago by • 0
50 results • Page 1 of 1
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Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Oh snap. Foiled again. Here it is with spaces & ge ; and & lt ;
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Oh LOL. My markdown got edited by the markdown editor! What is between the p and 50 in the first case is the HTML for greater than or equal…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Ah, good point. You could instead try ``` > library(ggtext) > keyvals.shape = c(rep(3,10), rep(2,8)) > names(keyvals.shape) = ifelse(keyva…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Hi, Yes, I've tried this, but I am not sure if it is possible to assign `bquote` values to the names of a vector. In particular, if I use…
Votes
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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