Showing : RNA • reset
0
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5
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481
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Help with DESeq results to pathways with the fgsea package
fgsea rna
updated 11 weeks ago by 65k • written 12 weeks ago by • 0
0
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1
reply
281
views
Running Deseq2 with all samples vs samples for each comparison separately
RNA DESeq2
updated 3 months ago by 41k • written 3 months ago by • 0
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2
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1.1k
views
Access Ensembl GRCH38 Version 87 Using BiomaRt
biomaRt ensembldb RNA ensembl
updated 13 months ago by ★ 2.0k • written 13 months ago by • 0
3
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6
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1.9k
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Limma: log2 of TMM values for RNA-Seq Analysis and PlotMDS()?
Log2 edgeR RNA limma Normalization
17 months ago Sara • 0
0
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0
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527
views
Correct GFF3 translation for FeatureCounts
RNASeq FeatureCounts Rna
18 months ago rridley3 • 0
1
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1
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707
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Confused about design for RNA seq experiment
RNAseq ExperimentData RNAseq123 RNA ExperimentalDesign
updated 19 months ago by ★ 4.1k • written 19 months ago by ▴ 30
0
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2
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834
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Rsubread align --R session aborts
RNA Alignment Rsubread
21 months ago • updated 20 months ago sreekalasn • 0
0
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0
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773
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Job: Scientist/Senior Scientist – Bioinformatics / Computational Biology
MassSpectrometryData RNA DifferentialExpression
20 months ago António Miguel de Jesus Domingues ▴ 510
2
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1
reply
1.0k
views
Error in RNAseq123 analysis, unexpected symbol.
RNAseq123 Rna
updated 22 months ago by 50k • written 22 months ago by • 0
1
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2
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1.6k
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Is it necessary to standardize Combat in R?
RNA Combat sva R
23 months ago takemoto • 0
1
vote
1
reply
781
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Description of the headers obtained from the Eligos2 output
methylation RNA native epitranscriptomics
updated 2.2 years ago by ▴ 90 • written 2.2 years ago by ▴ 10
0
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1
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868
views
Ensembl dataset version
tximport rna rnaseqGene biomaRt
updated 2.3 years ago by ★ 4.1k • written 2.3 years ago by • 0
0
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0
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593
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Cross-cultivar RNA-seq analysis
RNA Normalization
3.0 years ago nancy • 0
0
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4
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1.3k
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Fitting a continuous variable with batch effect using Limma. Also a question about normalization.
limma edgeR rna
3.1 years ago Nirad ▴ 10
0
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3
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2.2k
views
Pearson correlation between gene expression and phenotype
edgeR RNASeq
updated 3.4 years ago by 50k • written 3.5 years ago by ▴ 10
4
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3
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2.2k
views
How to resolve NAs when annotating a diff gene list with org.Hs.eg.db terms?
annotation rna
updated 3.5 years ago by 65k • written 3.6 years ago by ▴ 20
2
votes
7
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1.2k
views
Affycoretools package, HTA 2.0 annotation for non-coding RNA
affy rna hta2.0 r
updated 3.9 years ago by 65k • written 3.9 years ago by • 0
1
vote
1
reply
787
views
How to interpret coefficients of time course modeled data with DESeq2?
deseq2 RNA
updated 4.0 years ago by 41k • written 4.0 years ago by • 0
0
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6
replies
1.2k
views
Bizarre Dispersion Plots
deseq2 RNA RNASeq
updated 4.2 years ago by 41k • written 4.2 years ago by • 0
0
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0
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815
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Job: Post-doctoral Fellowship at BC Cancer Research Center, Vancouver BC
single cell RNA Data analysis Bioinformatics Job
4.8 years ago jmaanaki • 0
1
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1
reply
1.3k
views
how to filter genes in significant module?
RNA WGCNA filter
4.8 years ago modarzi ▴ 10
0
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2
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886
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DESeq and checkFullRank(modelMatrix)
RNA DESeq2
updated 5.0 years ago by 41k • written 5.0 years ago by ▴ 10
2
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1
reply
819
views
DESeq2 statistic and design
deseq2 RNA
updated 5.1 years ago by 41k • written 5.1 years ago by ▴ 10
5
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5
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1.4k
views
Association analysis between gene expression and Phenotype
rna singlecell limma
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 20
2
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3
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1.1k
views
Number and percent of mapped reads from RNA seq analysis.
rna-seq rna
updated 5.1 years ago by ★ 13k • written 5.1 years ago by ▴ 20
1
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0
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943
views
Job: 1 Computational Biologist and 1 Molecular Biologist
computational biology molecular biology RNA r-loop ncRNA Job
5.5 years ago l.brown ▴ 10
0
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0
replies
940
views
R code for finding wobble/redundant positions in an RNA string
r code rna wobble
6.2 years ago fawazfebin ▴ 60
0
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1
reply
987
views
Time series comparison with DESEQ2
RNA rnaseq deseq2
updated 6.7 years ago by 41k • written 6.7 years ago by ▴ 20
0
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1
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1.4k
views
RNA sequencing analysis for time point experiment using DeSeq2
deseq2 RNA rnaseq
updated 6.8 years ago by 41k • written 6.8 years ago by ▴ 20
1
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1
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1.3k
views
Outliers - to remove or to not remove that is the question
outliers rna microarray
updated 6.9 years ago by ▴ 420 • written 6.9 years ago by ▴ 30
5
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4
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1.3k
views
Experiment design contrasts any time edgeR
DGE rnaseq RNA edger
updated 7.0 years ago by • 0 • written 7.0 years ago by ▴ 40
3
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6
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1.9k
views
Regressing effect of treatment on RNA-seq expected count from rsem.
RNA rna-seq science bioinformatics
updated 7.0 years ago by 65k • written 7.0 years ago by ▴ 20
6
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5
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3.9k
views
Clustering differential expression results from voomWithQualityWeights
RNA limma rsem edgeR
updated 7.1 years ago by 50k • written 7.1 years ago by ▴ 20
0
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0
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1.5k
views
Finding candidate binding sites for RNA binding proteins in R
R bioconductor RNA mRNA RNA binding proteins
7.1 years ago Walter F. Baumann ▴ 10
3
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1
reply
1.7k
views
Targeted RNASeq/CaptureSeq DE Analysis
EdgeR deseq2 RNA differential expression
updated 7.6 years ago by ★ 28k • written 7.6 years ago by • 0
0
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4
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5.0k
views
RNAseq Adjusting for Covariates?
RNA rnaseq Covariate adjustment deseq
updated 8.2 years ago by 41k • written 8.2 years ago by • 0
0
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2
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1.3k
views
Normalizzation indipentent data from RNAAeq experiment
rna normalization
9.6 years ago aristotele_m ▴ 40
37 results • Page 1 of 1
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Comment: Deseq2 and Normalization of RNA sequencing data by ATpoint ★ 4.1k
There is no expectation of normality that is realistic in terms of expression level. Levels are widely different between genes, and counts …
Comment: Differences in differential analysis methods for RNA-Seq by ATpoint ★ 4.1k
MAGeCK is a command line tool that is easy to use. I recommend you use it because a) the logFCs from DESeq2 and MAGeCK will be very similar…
Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position) by Yveto • 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Answer: More regions in union when increasing DBA$config$mergeOverlap by Rory Stark ★ 5.2k
I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
Comment: log2FoldChange value is way too different when compared with counts(dds) by Michael Love 41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
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