Showing : RNAseq • reset
0
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3
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1.6k
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DeSeq2- design experiment
rnaseq degseq
8.0 years ago laksharikrish • 0
0
votes
3
replies
1.1k
views
Dseq single factor and 4 levels experiment design
rnaseq deseq2
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
5
votes
1
reply
3.2k
views
Difference between heatmap using Euclidian distance and Poisson distance
deseq2 euclidean sample distance rnaseq
updated 8.0 years ago by 43k • written 8.0 years ago by ▴ 20
0
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0
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793
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comparison of expression between orthologous species
rnaseq differential gene expression
8.0 years ago laksharikrish • 0
1
vote
2
replies
716
views
DE Analysis strategies for designs that are "not full rank"
deseq2 rnaseq
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
11
votes
3
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4.3k
views
Testing three-way interactions in DESeq2
deseq2 rna-seq rnaseq interactions
updated 8.0 years ago by 43k • written 8.0 years ago by ▴ 60
28
votes
7
replies
14k
views
Effect of lfcThreshold on p-value in DESeq2
deseq2 rnaseq statistics
updated 2.0 years ago by ▴ 10 • written 8.0 years ago by ▴ 40
5
votes
2
replies
1.7k
views
DESeq2 contrast give different results for same comparison using standard analysis
rnaseq deseq2
8.0 years ago Letícia ▴ 10
3
votes
0
replies
2.0k
views
What's the correct way to normalize HTseq files with TCGAbiolinks
normalization R rnaseq bioconductor
8.0 years ago eshelden ▴ 40
0
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2
replies
1.8k
views
creating design and count matrix for rna-seq differential expression
limma rnaseq edger
updated 8.0 years ago by ★ 29k • written 8.0 years ago by • 0
2
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1
reply
2.0k
views
SGSeq error on getBamInfo
SGSeq getBamInfo RNASeq
updated 8.0 years ago by ▴ 260 • written 8.0 years ago by ▴ 40
1
vote
11
replies
8.5k
views
RNA Seq data analysis using Salmon and tximport
RNAseq tximport
8.0 years ago tanyabioinfo ▴ 30
1
vote
3
replies
1.6k
views
DESeq: large difference in number of replicates per condition
deseq2 rnaseq differential expression
updated 8.0 years ago by 43k • written 8.0 years ago by ▴ 10
2
votes
4
replies
1.7k
views
Removing batch effect on edgeR when interactons are looked at
rnaseq edger statistics model matrix
updated 8.0 years ago by ★ 13k • written 8.0 years ago by ▴ 90
0
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1
reply
3.6k
views
NA values of count matrix in class DESeqDataSet
rnaseq recount
8.0 years ago maleknias • 0
25
votes
7
replies
13k
views
Different logFC (log2foldchange) values for genes from limma-voom and other tools (edgeR and DESeq2)
limma deseq2 edger rnaseq
updated 8.0 years ago by 53k • written 8.0 years ago by ▴ 20
10
votes
6
replies
5.5k
views
Bootstrap confidence intervals on RNA-seq expression from Kallisto
rnaseq deseq2 edger voom limma
updated 8.1 years ago by ▴ 110 • written 10.4 years ago by 21k
0
votes
1
reply
2.0k
views
DESeq2 biological replicates and RIN values
deseq2 differential gene expression covariates rnaseq
updated 8.1 years ago by 43k • written 8.1 years ago by • 0
0
votes
1
reply
904
views
differentially expressed genes form RSEM genes data
rnaseq edgeR
updated 8.1 years ago by 53k • written 8.1 years ago by ▴ 20
0
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1
reply
1.7k
views
RNA-Seq DEG analysis questions
rnaseq deg
updated 8.1 years ago by 53k • written 8.1 years ago by • 0
8
votes
3
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2.5k
views
Why edgeR::aveLogCPM() is simlar to log2(rowMeans(cpm)) instead of rowMeans(cpm(y, log=TRUE))
edgeR rnaseq limma independent filtering
8.1 years ago Robert Castelo ★ 3.4k
0
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0
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1.2k
views
Combined strand specific and unstranded samples
strand rnaseq differential gene expression batch effect counts
8.1 years ago lirongrossmann ▴ 80
5
votes
2
replies
4.6k
views
deseq2 LRT vs Wald test results for DE expression among 4 conditions
rnaseq deseq2 lrt wald differential gene expression
updated 3.5 years ago by • 0 • written 8.1 years ago by • 0
0
votes
1
reply
1.9k
views
Set rnaseq locial flag during GSVA
gsva rnaseq tpm
updated 8.1 years ago by ★ 3.4k • written 8.2 years ago by • 0
0
votes
2
replies
733
views
R script problem
R rnaseq bioconductor
updated 8.1 years ago by 68k • written 8.1 years ago by • 0
2
votes
2
replies
1.5k
views
Why does total unique map not equal to library size?
htseqcounts star rnaseq
8.1 years ago Ahdee ▴ 60
0
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7
replies
9.6k
views
Regarding scRNA seq vs Bulk RNA seq
single cell rnaseq
updated 8.1 years ago by ▴ 10 • written 8.1 years ago by • 0
2
votes
3
replies
3.8k
views
DESEq2 p-values weird distribution under the H0 and fdrtool
rnaseq deseq2 fdrtool differential gene expression
8.1 years ago tcalvo ▴ 100
1
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1
reply
2.6k
views
High variation among biological replicates. Options for correction during DE analysis
rnaseq
updated 8.1 years ago by ★ 29k • written 8.1 years ago by • 0
3
votes
3
replies
8.7k
views
Retrieving data from NCBI GEO Problem and RNA-Seq Data Analysis
rnaseq rna-seq limma geoquery edger
updated 8.2 years ago by 21k • written 8.2 years ago by ▴ 20
0
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1
reply
1.4k
views
Time series comparison with DESEQ2
RNA rnaseq deseq2
updated 8.2 years ago by 43k • written 8.2 years ago by ▴ 20
4
votes
8
replies
2.7k
views
Advice regarding RNAseq data with no replicates, best approach to accomplish fold-change
rnaseq edger DGE no replicates
8.2 years ago Stefany Solano • 0
5
votes
4
replies
2.1k
views
Testing for DE genes between samples of isolated cells, accounting for expression in whole tissue
limma rnaseq rna-seq model-matrix multiple factor design
updated 8.2 years ago by ★ 29k • written 8.2 years ago by ▴ 10
0
votes
2
replies
1.8k
views
DESeq2 multifactorialdesign contrasts
deseq2 rnaseq multifactorial design design and contrast matrix
updated 8.2 years ago by ▴ 690 • written 8.2 years ago by • 0
7
votes
3
replies
3.9k
views
Estimating cell size factors for single cell RNA-seq data
scrnaseq rnaseq normalization DESeq2
updated 8.2 years ago by 43k • written 8.2 years ago by ▴ 10
0
votes
3
replies
1.9k
views
Is the CPM filtering method from NOISeq unsupervised?
rnaseq de analysis gene filtering noiseq
updated 8.2 years ago by 68k • written 8.2 years ago by ▴ 50
2
votes
1
reply
1.5k
views
Read normalization in derfinder
derfinder normalization rnaseq
updated 8.2 years ago by ★ 1.1k • written 8.2 years ago by ▴ 10
0
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0
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1.4k
views
Polyester - creating simulated reads based on raw count matrix
polyester rnaseq simulation
8.2 years ago sseo2 • 0
0
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2
replies
1.9k
views
ggplots gives errors
rnaseq ggplot2
updated 8.2 years ago by ▴ 20 • written 8.2 years ago by • 0
3
votes
6
replies
23k
views
DESeq2: QQ plot of P-values
deseq2 rnaseq rna-seq
8.2 years ago nikmehr22 • 0
2
votes
1
reply
1.3k
views
Derinder options (species, annotations style)
derfinder rnaseq differential expression
updated 8.2 years ago by ★ 1.1k • written 8.2 years ago by ▴ 20
0
votes
0
replies
1.3k
views
Tools for classifying reads from xenograft samples?
rnaseq xenograph
8.2 years ago alakatos ▴ 130
1
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3
replies
2.8k
views
Annotate gene counts
annotation RNASeq annotationdbi
updated 8.2 years ago by 43k • written 8.2 years ago by • 0
0
votes
1
reply
1.7k
views
RNA sequencing analysis for time point experiment using DeSeq2
deseq2 RNA rnaseq
updated 8.2 years ago by 43k • written 8.2 years ago by ▴ 20
0
votes
5
replies
2.8k
views
[MnnCorrect] In case of known subpopulations
scran single-cell mnncorrect rnaseq
8.2 years ago Jens Preussner ▴ 30
0
votes
1
reply
2.2k
views
confusion with tximport options and resulting matrix
tximport rnaseq rsem limma voom
updated 8.2 years ago by 53k • written 8.2 years ago by • 0
0
votes
5
replies
3.6k
views
Load saved RangedSummarizedExperiment as Deseq2 dataset
deseq2 hdf5 rangedsummarizedexperiment rnaseq
8.2 years ago Jakob Petereit • 0
3
votes
11
replies
4.4k
views
DESeq function taking too long
deseq2 deseq factor rnaseq
updated 8.2 years ago by ★ 3.0k • written 8.2 years ago by ▴ 30
3
votes
7
replies
3.7k
views
deseq2 complex time course data with out replicates
deseq2 timecourse rnaseq
updated 8.2 years ago by ▴ 690 • written 8.2 years ago by • 0
1
vote
3
replies
2.6k
views
[DESeq2] time-course Experimental design
rnaseq deseq2 time-course
updated 8.2 years ago by ▴ 690 • written 8.2 years ago by ▴ 10
1,409 results • Page 16 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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