Showing : RNA-Seq • reset
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How to identify differentially expressed genes from Reactome pathways enriched according to GOseq?
goseq go rna-seq
5.5 years ago hasse.bossenbroek • 0
3
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5
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3.0k
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How to analyze pre-processed RNA-Seq data from GEO based on the deseq R package for filtering and DE analysis
deseq rna-seq filtering DE deseq2
updated 5.5 years ago by 43k • written 5.5 years ago by ▴ 840
3
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6
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2.7k
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paired and unpaired test at the same time with voom limma
limma voom rna-seq paired test unpaired test
updated 5.5 years ago by 53k • written 5.5 years ago by • 0
1
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4
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1.5k
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Nested paired design with covariates in limma
RNA-seq Nested paired design limma
updated 2.7 years ago by 53k • written 5.5 years ago by • 0
2
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3
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1.3k
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Drug response pre- and post-treatment between timepoints across conditions
RNA-seq Paired design Timecourse Diagnosis Covariates
updated 5.5 years ago by ★ 4.0k • written 5.5 years ago by • 0
8
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5
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4.2k
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How to know if I should use voomWithQualityWeights() or not?
limma RNA-Seq voom voomWithQualityWeights edgeR
updated 5.6 years ago by 53k • written 5.6 years ago by ▴ 10
4
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3
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1.2k
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RNA-Seq analysis with DESeq2: showing two conditions do *not* significantly differ
deseq2 RNA-Seq uniform distribution data visualization
updated 5.6 years ago by ★ 13k • written 5.6 years ago by ▴ 20
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1
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1.3k
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Adjusting for unwanted variation in DESeq2
DESeq2 deseq2 sva rna-seq differential expression anlaysis
updated 5.6 years ago by 68k • written 5.6 years ago by • 0
2
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4
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1.5k
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DEsingle differential-expression analysis
DEsingle RNA-seq differential-expression analysis
updated 5.6 years ago by ▴ 10 • written 5.9 years ago by ▴ 60
0
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3
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1.3k
views
DESeq2 accounting for two confounders with interaction in the design matrix
deseq2 design matrix multi-confounders linear models rna-seq
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
6
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6
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1.9k
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Design to analyze experiment with multiple samples from the same biological entity
rna-seq design linear model glm
updated 5.6 years ago by ★ 13k • written 5.6 years ago by • 0
0
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1
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2.6k
views
Error in .updateHubDB(hub_bfc, .class, url, proxy, localHub) :
annotation singlecell rna-seq
updated 5.7 years ago by 4.2k • written 5.7 years ago by • 0
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0
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1.1k
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Job: Bolzano, Italy: Post Doc Researcher in bioinformatics of cancer epigenomics
RNA-seq ChIP-seq Job
5.7 years ago Johannes Rainer ★ 2.1k
3
votes
11
replies
2.8k
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normalization methods for scRNA-seq and RNA-seq in specific cases of increased global transcription
RNA-seq scRNA-seq
updated 5.7 years ago by ★ 29k • written 5.7 years ago by ▴ 670
0
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4
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1.6k
views
GOexpress - Error when plotting expression data
RNA-seq transcriptomics gene ontology gene expression GOexpress
updated 5.7 years ago by ▴ 350 • written 5.7 years ago by • 0
0
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4
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1.2k
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Normalizing for both gene size and library composition
RNA-seq normalization deseq2
updated 5.7 years ago by 43k • written 5.7 years ago by ▴ 40
1
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2
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1.3k
views
Regularization of ballgown object on Limma
limma ballgown RNA-seq
5.7 years ago komuracom16 • 0
4
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8
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1.8k
views
problem in designing matrix and batch effect
edger rna-seq matrix
updated 5.7 years ago by 68k • written 5.7 years ago by • 0
0
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0
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1.3k
views
Job: Bioinformatician Positions at the University of Chicago BSD Bioinformatics Core
RNA-seq DNA-seq ATAC-seq proteomics microbiome Job
5.8 years ago lhuang7 ▴ 50
0
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3
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4.1k
views
Normalisation - Deseq2 vs StingTie-Ballgown
deseq2 StringTie RNA-seq normalisation
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
0
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0
replies
1.2k
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Normalisation of Data before loading in TMixClust
rna-seq tmixclust k-means clustering gene expression genesis
5.8 years ago astridite • 0
2
votes
4
replies
2.7k
views
Case-control study using WGCNA
wgcna network rna-seq
5.8 years ago Arindam ▴ 80
2
votes
11
replies
4.1k
views
Cannot find header.json in salmon index directory
salmon tximeta rna-seq
5.9 years ago • updated 5.8 years ago mico • 0
0
votes
1
reply
1.3k
views
problem for interpretation of resulted ComBat() plot
ComBat sva batch effect RNA-seq
updated 5.8 years ago by ▴ 870 • written 5.8 years ago by ▴ 10
2
votes
5
replies
1.5k
views
Nested Random Effect in LIMMA: Is It Possible?
limma rna-seq edger random effects
updated 5.8 years ago by 53k • written 5.8 years ago by • 0
0
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1
reply
1.5k
views
DESeq2 very complex design - how extract contrasts of interest?
DESeq2 RNA-Seq Multifactorial Design GLM Contrasts
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
0
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2
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2.3k
views
WGCNA module Eigengene PC1 and expression correlation
WGCNA DESeq2 RNA-Seq
5.9 years ago • updated 5.8 years ago Sri Dewi • 0
1
vote
10
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11k
views
DESeq2: Continuous and discreate variables in the design
deseq2 R rna-seq design
updated 10 weeks ago by 43k • written 5.9 years ago by • 0
3
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3
replies
1.1k
views
Nested Interaction in edgeR and composition bias
edger rna-seq
updated 5.9 years ago by 53k • written 5.9 years ago by • 0
1
vote
4
replies
1.9k
views
transcriptR ChIP-seq RNA-seq bam Error in mergeNamedAtomicVectors
TranscriptR RNA-seq ChIP-seq
updated 5.9 years ago by 68k • written 5.9 years ago by ▴ 10
8
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7
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7.8k
views
Further clarification on when not to use duplicateCorrelation with technical replicates (RNA-seq)
limma duplicateCorrelation rna-seq technical replicates biological replicates
updated 6.0 years ago by ★ 29k • written 6.0 years ago by ▴ 50
2
votes
1
reply
2.8k
views
Batch Corrections (MNN) with TPM values
scRNA-Seq scater scran rna-seq MNN
updated 6.0 years ago by ★ 29k • written 6.0 years ago by ▴ 60
0
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0
replies
956
views
ballgown -- how is statistical test performed
ballgown rna-seq
6.0 years ago michael • 0
0
votes
0
replies
918
views
ballgown: how to test for DE for my experimental setup
ballgown rna-seq
6.0 years ago michael • 0
0
votes
5
replies
1.9k
views
How to align to genome and transcriptome coordinates at the same time with STAR?
aligning ribosome profiling RNA-Seq
6.1 years ago Crispy • 0
0
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1
reply
637
views
Dispersion shrinkage in DESeq2: LOESS instead of negative binomial based GLM?
deseq2 RNA-Seq
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
5
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6
replies
1.9k
views
is our edgeR code doing what we think it does?
edger differential expression rna-seq
updated 6.1 years ago by ▴ 900 • written 6.1 years ago by ▴ 10
2
votes
3
replies
1.5k
views
Design for introducing batch effect in DESeq2
deseq2 combat batch effect rna-seq edger
updated 6.1 years ago by ★ 1.4k • written 6.1 years ago by ▴ 80
0
votes
2
replies
1.7k
views
How an index is built for each gene set collections using buildCustomIdx() indexing function of EGSEA package?
EGSEA edgeR biomaRt limma RNA-seq
6.1 years ago fgol ▴ 10
1
vote
4
replies
1.6k
views
gene Isoforms quantification using RNA-seq data
gene isoform quantification rna-seq
updated 6.1 years ago by ★ 1.4k • written 6.1 years ago by • 0
1
vote
1
reply
1.3k
views
How to perform RNA-seq with such MDS plot?
limma batch effect rna-seq
updated 6.1 years ago by ★ 1.4k • written 6.1 years ago by • 0
2
votes
7
replies
2.8k
views
RNA-seq with Salmon and tximport
RNA-seq Salmon tximport
updated 6.1 years ago by 68k • written 6.1 years ago by • 0
0
votes
1
reply
1.2k
views
How to arrange multiple plots into one page in NOISeq?
noiseq RNA-seq quality control
updated 16 months ago by • 0 • written 6.1 years ago by ▴ 80
0
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0
replies
1.8k
views
Job: Senior/Junior Bioinformatician - University of Massachusetts Medical School
single cell sequencing RNA-Seq ChIP-Seq ATAC-Seq Job
6.3 years ago • updated 6.1 years ago Julie Zhu ★ 4.3k
0
votes
3
replies
1.6k
views
How to apply a linear mixed model onto an RNA-Seq data?
limma linear mixed model voom rna-seq
6.1 years ago Assa Yeroslaviz ★ 1.5k
4
votes
8
replies
26k
views
Variance stabilising transformation for machine learning
deseq2 vst rna-seq machine-learning
updated 6.1 years ago by 43k • written 6.1 years ago by ▴ 20
5
votes
3
replies
1.6k
views
DESeq2 with multiple treatments but no replicates
deseq2 rna-seq
updated 6.2 years ago by 43k • written 6.2 years ago by ▴ 20
0
votes
4
replies
1.4k
views
coverageByTranscript coudble counts overlapped region for paired-end data
GenomicAlignments RNA-seq paired-end read coverage
updated 6.2 years ago by 16k • written 6.2 years ago by ▴ 90
0
votes
2
replies
1.4k
views
Problem in featureCounts file.
rna-seq featureCounts SubRead
updated 6.2 years ago by ★ 3.6k • written 6.2 years ago by • 0
2
votes
3
replies
2.1k
views
RNAseq and heatmap
deseq2 RNA-seq Heatmap
updated 6.2 years ago by 43k • written 6.2 years ago by ▴ 10
418 results • Page 3 of 9
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Answer: Gatins Set error by James W. MacDonald 68k
`GatingSet` isn't a function in `flowCore`. It is however in `flowWorkspace`, which you would need to load first.
Answer: How to model DE for RNA-seq in concordant monozygotic twins? by Gordon Smyth 53k
Your question is more about science than it is about software syntax, and I can't give advice about how to conduct a scientific analysis, n…
Comment: incomplete imputation of missing values with LEA impute() function by Gordon Smyth 53k
Nadia, please tag your question with the name of the package ("LEA") that you are asking about. "impute" is the name of a different Biocond…
Comment: Sharing a collection of datasets in ExperimentHub by Aaron Lun ★ 29k
FYI the **scRNAseq** packages uses a non-ExperimentHub storage platform, see [here](https://github.com/ArtifactDB/gypsum-worker) for more d…
Comment: Error Loading Experiment from SimBenchData Package by ATpoint ★ 4.9k
Is the Seurat package installed? The error somewhat suggests that it could be related, and at https://www.bioconductor.org/packages/release…
Votes
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
Answer: ordinary t from limma [was: How would I normally compare swirl?]
Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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