Showing : RNAseq • reset
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DESeq2 - Design for TCGA unpaired RNAseq data
DESeq2 design TCGA unpaired RNAseq
updated 7.7 years ago by 43k • written 7.7 years ago by ▴ 10
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Job: Bioinformatician/Biostatistician - Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), Mainz, Germany
rnaseq biostatistics bioinformatician next-generation sequencing Job
7.8 years ago Federico Marini ▴ 180
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1.4k
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Error with tximport on Kallisto .h5 data.
tximport kallisto bioconductor rnaseq
7.8 years ago srdjan.kasapovic0 • 0
9
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6
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2.5k
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Representative gene expression value in one condition with several replicates
rnaseq gene expression edger
updated 7.8 years ago by 53k • written 7.8 years ago by ▴ 20
0
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1
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1.8k
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AnnotationForge, RNAseq, and non-model organism
AnnotationForge annotationforge nonmodel rnaseq
updated 7.8 years ago by 68k • written 7.8 years ago by • 0
0
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2
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1.3k
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Single and double mutant DEG analysis using DESeq2
deseq2 batch effect rnaseq
updated 7.8 years ago by 43k • written 7.8 years ago by • 0
0
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0
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1.5k
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Job: Bioinformatics Analyst II/III - Banchereau Lab @ The Jackson Laboratory
rnaseq atac-seq iso-seq chipseq Job
7.8 years ago tyler.chukwu • 0
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0
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1.4k
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Understanding NextMaSigPro, regression fit and stepwise regression
timecourse rnaseq masigpro
7.8 years ago jelisaveta.jeki.djordjevic • 0
3
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1
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1.4k
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Applying replaceOutliers rather than throwing out genes when model includes continuous variable
deseq2 rnaseq differential gene expression differential expression
updated 7.8 years ago by 43k • written 7.8 years ago by • 0
0
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1
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748
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Extreme log2 FC from DESeq2
rnaseq deseq2
updated 7.8 years ago by 43k • written 7.8 years ago by • 0
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0
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1.8k
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DEXseq: error using DEXSeqDataSetFromSE command
rnaseq dexseq summarizedexperiment
7.9 years ago f.carlisle • 0
6
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6
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9.2k
views
EdgeR design matrix with 3 factors
edger glm rnaseq
7.9 years ago Denniswu ▴ 20
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9
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2.4k
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Loads, really loads of DEGs after edgeR differential analysis
rnaseq edger normalization differential gene expression
7.9 years ago David R ▴ 90
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3
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1.6k
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Choosing DESeq2 design for mice experiment
deseq2 mouse rnaseq
7.9 years ago Emilie • 0
4
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15
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5.3k
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DESeq2 for mulitple tissues under 2 conditions and contrast options
deseq2 rnaseq featurecounts DESeqDataSetFromMatrix
updated 7.9 years ago by 43k • written 8.0 years ago by ▴ 10
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0
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1.5k
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Job: Computational Biology/Bioinformatics Post-doctoral position, Johns Hopkins University, Baltimore, USA
rnaseq next-generation sequencing database Job
7.9 years ago cleo.k.yang • 0
4
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6
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2.2k
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RNA-Seq : zero counts
rnaseq bioconductor
updated 7.9 years ago by 68k • written 7.9 years ago by ▴ 120
6
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11
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4.2k
views
Error and weird result of TCGAanalyze_Normalization function using the R package TCGAbiolinks for normalization of raw HTSeq counts
tcgabiolinks rnaseq normalization EDASeq
updated 7.9 years ago by ▴ 50 • written 7.9 years ago by ▴ 840
2
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9
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2.0k
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SNP-level Allele-specific expression detection using DESeq2 in an unpaired experimental design
deseq2 rnaseq differential gene expression
7.9 years ago engelbrecht.stephan ▴ 10
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1.7k
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Specific considerations in RNA-Seq DE analysis with edgeR pipeline for a TCGA dataset starting with HTSeq counts
edgeR rnaseq DEanalysis TCGA independent filtering
7.9 years ago svlachavas ▴ 840
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3
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1.7k
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DESeq2 with categorical variables only in treatment group (not in controls)
rnaseq deseq2 categorical
updated 7.9 years ago by 43k • written 7.9 years ago by • 0
1
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2
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2.3k
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DESeq2 for differential gene expression on GTEx dataset
rnaseq deseq2 gtex
updated 7.9 years ago by 43k • written 7.9 years ago by • 0
5
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4
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9.8k
views
Choosing a threshold for minimum counts in RNAseq
rnaseq deseq2
updated 7.9 years ago by 43k • written 9.4 years ago by ▴ 20
0
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3
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2.3k
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Interpretation of the log fold change for a time course/factorial design analysis in limma
limma rnaseq multifactorial design multiple time points
updated 7.9 years ago by ★ 29k • written 7.9 years ago by • 0
4
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3
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1.6k
views
RNASeq interaction between factors with edgeR when cpms tend to zero
rnaseq edgeR edger main and interaction effects
7.9 years ago David R ▴ 90
3
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5
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1.8k
views
DESeq2 biais when genes are missing from the annotation?
rnaseq deseq2
updated 7.9 years ago by 43k • written 7.9 years ago by • 0
0
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12
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2.4k
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DESeq2 different versions
rnaseq r deseq2
updated 7.9 years ago by 43k • written 7.9 years ago by • 0
1
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7
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2.0k
views
Strange distribution of logFC
edger deseq2 rnaseq differential gene expression
updated 7.9 years ago by ★ 29k • written 7.9 years ago by ▴ 20
0
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1
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2.2k
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Ballgown with replicates and the adjustvars option
ballgown rnaseq differential gene expression
updated 7.9 years ago by ▴ 210 • written 8.2 years ago by • 0
1
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3
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2.0k
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Pathway analysis from list of differentially expressed genes with fold change, pvalues and normalised expression levels in R
rnaseq pathway analysis R limma
updated 7.9 years ago by ▴ 760 • written 7.9 years ago by • 0
0
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2
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3.8k
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Design of 'group' object in DGElist function
egder dgelist group rnaseq
updated 7.9 years ago by ★ 29k • written 7.9 years ago by ▴ 60
4
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5
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2.1k
views
RNA Seq analysis vs. Single cell RNA seq analysis
rnaseq scrnaseq edger
8.0 years ago • updated 7.9 years ago fawazfebin ▴ 60
0
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14
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5.3k
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Using name parameter in DESeq2-results function
deseq2 rnaseq
7.9 years ago muratcokol • 0
5
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7
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8.5k
views
DESeq2 dispersion and p-value histograms
deseq2 rnaseq fdrtool dispersion
updated 8.0 years ago by ▴ 610 • written 8.0 years ago by ▴ 70
1
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3
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2.9k
views
Pathview pathview kegg.native=TRUE throws error in img
pathview kegg error bioconductor rnaseq
updated 8.0 years ago by ▴ 40 • written 8.6 years ago by ▴ 30
3
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1
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3.0k
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Explainnation of featureCounts in-built annotation?
rnaseq annotation featurecounts
updated 8.0 years ago by ★ 3.6k • written 8.0 years ago by ▴ 20
2
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8
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3.7k
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comparing strand-specific counts to unstranded counts
rnaseq strand deseq2
8.0 years ago lirongrossmann ▴ 80
0
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1
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736
views
Deseq2 group comparison
rnaseq deseq2
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
3
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1
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1.6k
views
featureCounts in-built annotation doesn't match BioMart annotation?
rnaseq annotation featurecounts biomart
updated 8.0 years ago by 68k • written 8.0 years ago by ▴ 20
0
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1
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1.3k
views
Running model separately for each cell line or as the same model?
limma deseq2 edger rnaseq
updated 8.0 years ago by ▴ 120 • written 8.0 years ago by ▴ 60
2
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1
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1.2k
views
Is my design appropriate for contrast in DESeq2?
deseq2 design and contrast matrix rnaseq
updated 8.0 years ago by ▴ 690 • written 8.0 years ago by • 0
1
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3
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5.6k
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Log2 fold change value in DESeq2
deseq2 rnaseq
written 8.0 years ago by • 0
2
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3
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4.8k
views
Deseq2: padj value changes with varying alpha
deseq2 counts rnaseq
updated 8.0 years ago by 43k • written 8.0 years ago by ▴ 10
0
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4
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2.6k
views
DEseq2: any problem with unbalanced number of sample in normal/tumor study?
deseq2 rnaseq tcga
updated 8.0 years ago by 43k • written 8.0 years ago by ▴ 60
1
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4
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2.4k
views
expression matrix with varianceStabilizingTransformation
deseq2 variancestabilizingtransformation rnaseq
updated 8.0 years ago by 43k • written 8.0 years ago by ▴ 80
6
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6
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13k
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Why different filtering criteria using CPM to filter the RNA-seq count data in edgeR have so much influence on the number of DE genes?
rnaseq edger
8.0 years ago Jack ▴ 20
4
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8
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2.2k
views
When doing differential gene analysis, why measuring genes based on exons? Can we measure genes based on CDS?
rnaseq featurecounts edger deseq2
updated 8.0 years ago by 53k • written 8.0 years ago by ▴ 20
0
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2
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1.9k
views
GO analysis under-represented genes and over-represented (enrichment) down-regulated genes
go rnaseq clusterprofiler topgo
8.0 years ago Jack ▴ 20
0
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3
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1.7k
views
replicates and groups of samples: what's the right DESeq2 model?
deseq2 rnaseq differential gene expression
updated 8.0 years ago by ▴ 690 • written 8.0 years ago by • 0
1
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8
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2.3k
views
Strange MA plot
rnaseq deseq2
updated 8.0 years ago by 43k • written 8.0 years ago by ▴ 20
1,409 results • Page 15 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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