Showing : RNAseq • reset
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DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
23 months ago erika.maldonado-rosado • 0
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0
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715
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is Dada2 biased toward a particular sequence ?
virology dada2 amplican Sequencing RNASeq
23 months ago Sara • 0
0
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2
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1.1k
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Will DESeq2 be appropriate tool for analysis?
RNASeq DESeq2
24 months ago • updated 23 months ago Karthik • 0
0
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0
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699
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Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
24 months ago Florian • 0
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0
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927
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Pysam pileup and Rsamtools pileup output discrepancy
Pysam pileup Rsamtools RNASeq
24 months ago Xinqi • 0
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0
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790
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Using DADA2 for finding viral sequence variants
VariantDetection dada2 RNASeq
24 months ago Sara • 0
1
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1
reply
995
views
Multiple comparison using DESeq2
RNASeqData RNASeq DESeq2
updated 24 months ago by 68k • written 24 months ago by • 0
1
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7
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1.7k
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DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 22 months ago by 53k • written 2.0 years ago by • 0
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2
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807
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Issues with ddseq2 for treatment response factoring in different KO clones
Clonality RNASeq DESeq2
updated 2.0 years ago by ★ 1.4k • written 2.0 years ago by • 0
0
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1
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1.0k
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Comparing RNASeq data from multiple studies
RNASeqData RnaSeqSampleSize RNASeqPower RNASeq
updated 2.0 years ago by ▴ 780 • written 2.0 years ago by • 0
3
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5
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2.1k
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Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 2.1 years ago by ★ 5.0k • written 2.1 years ago by • 0
1
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1
reply
890
views
bulk RNA-Seq batch correction
RNASeqData rnaseqcomp RNASeq
updated 2.1 years ago by ★ 5.0k • written 2.1 years ago by • 0
0
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1
reply
831
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DESeq design and contrast with multiple factors
RNASeq DESeq2
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
1
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6
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3.3k
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Time-series RNA-seq analysis using DESeq2
time-series DESeq2 RNASeq timecoursedata TimeCourse
updated 2.1 years ago by ★ 5.0k • written 2.1 years ago by • 0
6
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7
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1.5k
views
Adding a group of samples reduces DEGs in other groups
RNASeq limma
updated 2.2 years ago by 53k • written 2.2 years ago by ▴ 10
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1
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5.1k
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Is it proper to compare two WGCNA matrixes if they were raised to different power (soft threshold)?
Network cluster WGCNA RNASeq
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
2
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1
reply
1.2k
views
Grouping DEGs yields varying results
RNASeq limma
updated 2.2 years ago by 53k • written 2.2 years ago by ▴ 10
2
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5
replies
2.0k
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Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R edgeR RNASeq
2.2 years ago mohammedtoufiq91 ▴ 10
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2
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1.2k
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Correct DESeq2 design for tumoral stage differences in tumoral and matched-normal samples
DifferentialExpression RNASeq DESeq2
2.2 years ago Matteo • 0
4
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2
replies
3.1k
views
Gene set analysis: GSVA, Z-Score, and fold-changes
GSVA RNASeq limma
updated 2.3 years ago by 53k • written 2.3 years ago by ▴ 10
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3
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1.5k
views
Multiple Testing When Using Multiple Contrasts/Comparisons in DESEQ2
MultipleComparison DESeq2 Genetics contrasts RNASeq
updated 2.2 years ago by 68k • written 2.3 years ago by • 0
3
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11
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4.7k
views
Adjusting for baseline when having longitudinal data, mixed model and no treatment
RNAseq mixedmodels baselineadjustement limma
2.4 years ago • updated 2.3 years ago Anna ▴ 20
2
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9
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6.9k
views
how to control age and gender effect in expression data using DESeq2
deseq2 rnaseq mirna-seq differential gene expression
written 7.6 years ago by ▴ 10
0
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1
reply
853
views
CI for logCPM (fitted values)
RNAseq edgeR
updated 2.4 years ago by 53k • written 2.4 years ago by ▴ 10
3
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4
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1.1k
views
Anova table edgeR limma
limma RNASeq edgeR
2.4 years ago KATHERINE CHUERE NUNES • 0
1
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2
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1.0k
views
Obtention of the binomial transformed count table with edgeR
DESeq2 edgeR RNASeq DifferentialExpression
updated 2.4 years ago by 53k • written 2.4 years ago by • 0
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3
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1.4k
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Account for heteroscedasticity when fitting gene expression data
RNAseq
updated 2.4 years ago by 43k • written 2.4 years ago by • 0
1
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3
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1.5k
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Is it okay to increase filtering to get more significant Adjusted P Values for DEGs found using Limma?
RNASeqPower edgeR DifferentialExpression limma RNASeq
updated 2.4 years ago by 53k • written 2.4 years ago by • 0
0
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2
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2.4k
views
model matrix not full rank
DESeq2 RNASeq
updated 2.4 years ago by • 0 • written 2.4 years ago by • 0
0
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1
reply
996
views
What is the correct way to split genex_high and genex_low groups for DE analysis?
DESeq2 RNASeq
updated 2.4 years ago by 43k • written 2.5 years ago by • 0
2
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3
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827
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RNA seq with edgeR with several factors
RNAseq factors
2.5 years ago • updated 2.4 years ago Nathalie ▴ 20
0
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3
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1.3k
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edgeR DEGs multilevel
edgeR RNASeq DifferentialRegulation
updated 2.5 years ago by 53k • written 2.5 years ago by • 0
8
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10
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17k
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GSEA preranked analysis downstream of DEseq2
deseq2 gsea rnaseq
updated 5 months ago by ★ 5.0k • written 9.2 years ago by ▴ 20
0
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4
replies
1.7k
views
Combine RNA-seq
BatchEffect R rnaseq
updated 2.5 years ago by ★ 1.4k • written 2.5 years ago by • 0
1
vote
1
reply
693
views
Using R to measure differential gene expression of one gene due to different treatments using RNASeq counts
DESeq2 edgeR RNAseq
updated 2.5 years ago by 53k • written 2.5 years ago by • 0
3
votes
12
replies
2.8k
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 2.5 years ago by 43k • written 2.5 years ago by ▴ 10
0
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1
reply
739
views
Sample expression calculation in rna seq
Rnaseq
updated 2.5 years ago by ★ 5.0k • written 2.5 years ago by • 0
1
vote
1
reply
880
views
Can I run deseq2 on two separate experiments at once?
rnaseq deseq2
updated 2.5 years ago by ★ 5.0k • written 2.5 years ago by • 0
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0
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932
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WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome RNAseq WGCNA
2.5 years ago Levi • 0
4
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8
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6.0k
views
Interpreting ellipses in PCAtools for bulk RNAseq
ellipse RNAseq PCAtools
updated 2.5 years ago by • 0 • written 4.4 years ago by • 0
1
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2
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978
views
RNA-Seq normalization of pre and post treatment groups
Normalization RNASeq
written 2.5 years ago by • 0
2
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4
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1.4k
views
limma with or without intercept gives different results
limma rnaseq
2.5 years ago Sydney • 0
1
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2
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1.7k
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RUVSeq and DESeq2 -- all variables in design formula must be columns in colData
DESeq2 RNAseq RUVSeq
2.5 years ago garbuzov • 0
0
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2
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1.2k
views
Compare and filter three BAM files
RNAseq 10X
2.5 years ago wt215 • 0
0
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5
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1.6k
views
hill-shaped p-value distributions using EdgeR
edgeR p-valuedistribution RNAseq hill-shaped
updated 2.6 years ago by 53k • written 2.6 years ago by • 0
5
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7
replies
1.6k
views
different number of DEG because of outliers
DESeq2 RNASeq
updated 21 months ago by 53k • written 2.6 years ago by • 0
0
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2
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1.5k
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GO analysis in R vs website
GO RNASeq
2.6 years ago Nitro • 0
1
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4
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1.3k
views
Repeated Measures-Cross Over Study for RNAseq data using variancePartition::dream
RNAseq variancePartition edgeR dream
2.6 years ago DH • 0
1
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0
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1.2k
views
Job: Seeking collaborator/contractor (paid) for Bioconductor package development
RNASeq JobPosting
2.6 years ago Jamie Walters ▴ 10
3
votes
2
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1.5k
views
Batch question Bulk RNA-Seq
BatchEffect RNASeq
2.6 years ago chf • 0
1,409 results • Page 3 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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