Showing : RNAseq • reset
5
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6
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1.4k
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limma code for RNA-seq analysis (paired design)
limma rnaseq
updated 9.3 years ago by ★ 13k • written 9.3 years ago by ▴ 670
1
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0
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2.4k
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Job: Bioinformatics Scientist @ Berlin Institute for Medical Systems Biology
rnaseq snp chipseq Job
9.4 years ago altuna akalin ▴ 20
2
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3
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2.0k
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RNAseq outlier is a critical sample
rnaseq outlier statistics batch effect
updated 9.4 years ago by 53k • written 9.4 years ago by • 0
1
vote
2
replies
2.1k
views
edgeR | paired samples | multiple baseline | averaging baseline or not
edger rnaseq baseline linear model negative binomial model
updated 9.4 years ago by 53k • written 9.6 years ago by • 0
4
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7
replies
3.1k
views
RNAseq reads mapped to the gene
star featurecounts edgeR RNAseq
9.4 years ago myprogramming2016 • 0
1
vote
4
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2.2k
views
GOSeq: analysis of unsupported genome after HTseq and DEseq2 - building gene lengths, comparing contrasts and understanding results.
deseq2 goseq htseqcounts rnaseq plant
updated 9.4 years ago by 53k • written 9.4 years ago by • 0
52
votes
20
replies
51k
views
Batch correction in DESeq2
rnaseq batch effect deseq2 combat removebatcheffect()
updated 9.4 years ago by • 0 • written 9.8 years ago by ▴ 110
0
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7
replies
2.4k
views
Using Polyester to simulate large number of reads from a large transcriptome
polyester rnaseq
updated 9.4 years ago by ▴ 10 • written 9.4 years ago by • 0
0
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1
reply
1.4k
views
Problem installing Bioc Workflows
rnaseq workflows bioconductor
9.4 years ago Hadi Gharibi • 0
2
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3
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1.1k
views
DEGs : finding DE genes specific for one condition
deseq2 R rnaseq
9.4 years ago alva.james • 0
2
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6
replies
3.8k
views
Clustering and bootstrapping of RNASeq samples
clustering pvclust vsd edgeR rnaseq
written 9.4 years ago by ▴ 90
1
vote
1
reply
2.4k
views
Null model in SVA for patient paired test comparing tumor vs normal
sva paired samples rnaseq
updated 9.4 years ago by ▴ 650 • written 9.4 years ago by • 0
2
votes
2
replies
2.6k
views
"U" shaped p values distribution in DESeq2 RNA-seq DE analysis using the contrast argument
deseq2 rnaseq contrast multiple comparisons fdrtool
9.4 years ago sebastiano.curreli • 0
4
votes
5
replies
1.4k
views
DESeq2 how to define my conditions when I want the results comparing a subset of samples
deseq2 rnaseq
updated 9.4 years ago by ★ 7.9k • written 9.4 years ago by ▴ 10
0
votes
0
replies
2.0k
views
GOseq tutorial for not supported organisms: am I doing it correctly?
deseq2 goseq biomart r rnaseq
9.4 years ago CandiceChuDVM ▴ 40
1
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3
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3.2k
views
DESeq normalization seems to reverse the directionality of log2FoldChange - is this normal?
deseq2 rnaseq rna-seq normalization cpm
updated 9.4 years ago by ★ 13k • written 9.4 years ago by • 0
0
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0
replies
966
views
normalizing gene expression data with TCGAbiolinks
microarray tcgabiolinks rnaseq
9.4 years ago Fernando • 0
3
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5
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9.1k
views
Wgcna with missing values - error with calculation of bicor correlations in pickSoftThreshold and blockwiseModules
software error rnaseq wgcna missing data
9.8 years ago • updated 9.4 years ago dvillarlozano ▴ 10
1
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2
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1.7k
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Normalized count or Count data for ToPASeq package
rnaseq Topaseq
9.5 years ago saamar.rajput • 0
6
votes
12
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20k
views
Problem making DESeq dataset; Error all variables in design formula must be columns in colData
deseq2 deseq counts rnaseq differential gene expression
updated 9.5 years ago by 43k • written 9.5 years ago by ▴ 10
0
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1
reply
1.8k
views
DESeq2 followed by Reporting tools lists blank ensemble gene ID's and symbols but has image, logFC and p-value intact in HTML file
deseq2 rnaseq reportingtools
updated 9.5 years ago by 43k • written 9.5 years ago by • 0
2
votes
6
replies
1.9k
views
Using edgeR with "traditional" coverage data?
edger rnaseq coverage
updated 9.5 years ago by ★ 7.9k • written 9.5 years ago by • 0
9
votes
6
replies
13k
views
Error bars DESeq or DESeq2 fold change
rnaseq deseq2 deseq standard error confidence interval
updated 3.9 years ago by 43k • written 9.5 years ago by ▴ 10
0
votes
0
replies
1.5k
views
error while running MAplot
MAplot rnaseq cummerbund
9.5 years ago kritikamish99 ▴ 10
7
votes
18
replies
4.7k
views
RNA-seq analysis using EdgeR- I need to make sure that the codes that I use to analyze the data are correct
rnaseq edger differential gene expression
updated 9.5 years ago by ★ 7.9k • written 9.6 years ago by • 0
0
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0
replies
1.7k
views
Annotation, Over representation testing and Pathway analysis using Ensembl gene IDs
rnaseq annotation gostats org.Bt.eg.db
9.5 years ago mrodrigues.fernanda ▴ 10
0
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0
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1.7k
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Job: Bioinformatics Postdoc in Functional Evolutionary Genomics, Heidelberg, Germany
rnaseq genomics evolution Job
9.5 years ago henrik.kaessmann • 0
1
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2
replies
1.6k
views
Multiple transcription factors over expression analysis
deseq2 rnaseq
9.5 years ago sebastiano.curreli • 0
0
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2
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5.3k
views
PlotMA Filters for DeSEQ2 ; adjusting script
deseq2 rnaseq plotMA deseq rna-seq
updated 9.6 years ago by 43k • written 9.6 years ago by • 0
0
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4
replies
4.8k
views
Using DESeq2 inside Galaxy
rnaseq galaxy deseq2
updated 9.6 years ago by 43k • written 9.6 years ago by ▴ 70
0
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2
replies
1.1k
views
RNAseq_Rsubread_transcript variants detection
rnaseq
updated 9.6 years ago by • 0 • written 9.6 years ago by ▴ 10
0
votes
4
replies
2.2k
views
Splicemap (in QuasR) failed while aligning 25mers
QuasR rnaseq alignment splicemap bowtie2
9.6 years ago Gabriella • 0
0
votes
4
replies
1.7k
views
is it possible to create this comparison?
rnaseq pairwise multiple comparisons deseq2
updated 9.6 years ago by 43k • written 9.6 years ago by • 0
2
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2
replies
2.3k
views
Normalization in edgeR
edger rnaseq bioconductor
updated 9.6 years ago by 53k • written 9.6 years ago by • 0
0
votes
4
replies
5.6k
views
RNAseq Adjusting for Covariates?
RNA rnaseq Covariate adjustment deseq
updated 9.6 years ago by 43k • written 9.6 years ago by • 0
0
votes
5
replies
2.1k
views
Normalisation of RNA seq data
rnaseq bioconductor R normalization
updated 9.6 years ago by ▴ 420 • written 9.6 years ago by ▴ 70
1
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6
replies
2.3k
views
how to deal the effect of enormous gene expression?
deseq2 rnaseq tomato geneexpression
updated 9.6 years ago by 43k • written 9.6 years ago by • 0
1
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3
replies
1.2k
views
Grouping similar genes in differential expression analysis to increase power
deseq2 rnaseq differential gene expression
updated 9.6 years ago by 43k • written 9.6 years ago by • 0
0
votes
1
reply
1.5k
views
Using Gage and pathview with previously processed data
pathview gage r kegg rnaseq
updated 9.6 years ago by ★ 1.6k • written 9.6 years ago by • 0
4
votes
12
replies
6.0k
views
remove batch effect using limma
limma rnaseq batch effect pearsoncorrelation
updated 9.6 years ago by ★ 29k • written 9.6 years ago by • 0
0
votes
1
reply
1.3k
views
No reads with summarizeOverlaps
summarizeoverlaps rnaseq
9.6 years ago diogo.camacho.2008 • 0
1
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1
reply
2.7k
views
edgeR GLM fitted values
edgeR GLM classification rnaseq
updated 9.6 years ago by ★ 29k • written 9.6 years ago by ▴ 10
1
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8
replies
1.4k
views
The same statistical test for all multi omic features
limma microarray rnaseq deseq2
9.7 years ago chris86 ▴ 420
1
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2
replies
1.4k
views
EdgeR GLM following voom conversion of counts
limma voom edger rnaseq
updated 9.7 years ago by ★ 7.9k • written 9.7 years ago by • 0
0
votes
0
replies
2.0k
views
Hierarchical Random Forest classifier
rnaseq machinelearning random forest mlseq
9.7 years ago anthony.hawkins ▴ 10
0
votes
2
replies
4.0k
views
Using sva ComBat on DESeq2 Data
deseq2 DE rnaseq sva combat
updated 9.7 years ago by 43k • written 9.7 years ago by • 0
2
votes
1
reply
1.8k
views
no DGE with multiple groups in edge R
edgeR differential gene expression RNAseq
updated 9.7 years ago by ★ 29k • written 9.7 years ago by ▴ 20
1
vote
2
replies
7.3k
views
HTseq in bioconductor
rnaseq bioconductor
9.7 years ago KB ▴ 50
1
vote
1
reply
13k
views
Deseq2 for RNAseq experiments without replicates
rnaseq deseq2
updated 9.7 years ago by 43k • written 9.7 years ago by • 0
0
votes
3
replies
1.9k
views
RNAseq_alignment_SpliceMap processing time_QuasR
SpliceMap QuasR RNAseq Alignment
updated 9.7 years ago by ▴ 400 • written 9.7 years ago by ▴ 10
1,409 results • Page 21 of 29
Recent ...
Replies
Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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