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
5.6 years ago hasse.bossenbroek • 0
3
votes
5
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3.1k
views
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 5.6 years ago by 43k • written 5.6 years ago by ▴ 840
3
votes
6
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2.8k
views
paired and unpaired test at the same time with voom limma
limma voom rna-seq paired test unpaired test
updated 5.7 years ago by 53k • written 5.7 years ago by • 0
1
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4
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1.6k
views
Nested paired design with covariates in limma
RNA-seq Nested paired design limma
updated 2.8 years ago by 53k • written 5.7 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 5.7 years ago by ★ 4.0k • written 5.7 years ago by • 0
8
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5
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4.3k
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How to know if I should use voomWithQualityWeights() or not?
limma RNA-Seq voom voomWithQualityWeights edgeR
updated 5.7 years ago by 53k • written 5.7 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 5.7 years ago by ★ 13k • written 5.7 years ago by ▴ 20
0
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1
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1.4k
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Adjusting for unwanted variation in DESeq2
DESeq2 deseq2 sva rna-seq differential expression anlaysis
updated 5.7 years ago by 68k • written 5.7 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 5.7 years ago by ▴ 10 • written 6.0 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 5.7 years ago by 43k • written 5.7 years ago by • 0
6
votes
6
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1.9k
views
Design to analyze experiment with multiple samples from the same biological entity
rna-seq design linear model glm
updated 5.8 years ago by ★ 13k • written 5.8 years ago by • 0
0
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1
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2.7k
views
Error in .updateHubDB(hub_bfc, .class, url, proxy, localHub) :
annotation singlecell rna-seq
updated 5.8 years ago by 4.2k • written 5.8 years ago by • 0
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
5.8 years ago Johannes Rainer ★ 2.1k
3
votes
11
replies
2.9k
views
normalization methods for scRNA-seq and RNA-seq in specific cases of increased global transcription
RNA-seq scRNA-seq
updated 5.8 years ago by ★ 29k • written 5.8 years ago by ▴ 670
0
votes
4
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1.6k
views
GOexpress - Error when plotting expression data
RNA-seq transcriptomics gene ontology gene expression GOexpress
updated 5.8 years ago by ▴ 350 • written 5.8 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 5.8 years ago by 43k • written 5.8 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
5.8 years ago komuracom16 • 0
4
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8
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1.9k
views
problem in designing matrix and batch effect
edger rna-seq matrix
updated 5.9 years ago by 68k • written 5.9 years ago by • 0
0
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0
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1.4k
views
Job: Bioinformatician Positions at the University of Chicago BSD Bioinformatics Core
RNA-seq DNA-seq ATAC-seq proteomics microbiome Job
5.9 years ago lhuang7 ▴ 50
0
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3
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4.2k
views
Normalisation - Deseq2 vs StingTie-Ballgown
deseq2 StringTie RNA-seq normalisation
updated 5.9 years ago by 43k • written 5.9 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
5.9 years ago astridite • 0
2
votes
4
replies
2.8k
views
Case-control study using WGCNA
wgcna network rna-seq
6.0 years ago Arindam ▴ 80
2
votes
11
replies
4.2k
views
Cannot find header.json in salmon index directory
salmon tximeta rna-seq
6.0 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 6.0 years ago by ▴ 870 • written 6.0 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 6.0 years ago by 53k • written 6.0 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 6.0 years ago by 43k • written 6.0 years ago by • 0
0
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2
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2.4k
views
WGCNA module Eigengene PC1 and expression correlation
WGCNA DESeq2 RNA-Seq
6.0 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 3 months ago by 43k • written 6.0 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 6.1 years ago by 53k • written 6.1 years ago by • 0
1
vote
4
replies
2.0k
views
transcriptR ChIP-seq RNA-seq bam Error in mergeNamedAtomicVectors
TranscriptR RNA-seq ChIP-seq
updated 6.1 years ago by 68k • written 6.1 years ago by ▴ 10
8
votes
7
replies
8.0k
views
Further clarification on when not to use duplicateCorrelation with technical replicates (RNA-seq)
limma duplicateCorrelation rna-seq technical replicates biological replicates
updated 6.1 years ago by ★ 29k • written 6.1 years ago by ▴ 50
2
votes
1
reply
2.9k
views
Batch Corrections (MNN) with TPM values
scRNA-Seq scater scran rna-seq MNN
updated 6.1 years ago by ★ 29k • written 6.1 years ago by ▴ 60
0
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0
replies
988
views
ballgown -- how is statistical test performed
ballgown rna-seq
6.2 years ago michael • 0
0
votes
0
replies
948
views
ballgown: how to test for DE for my experimental setup
ballgown rna-seq
6.2 years ago michael • 0
0
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5
replies
1.9k
views
How to align to genome and transcriptome coordinates at the same time with STAR?
aligning ribosome profiling RNA-Seq
6.2 years ago Crispy • 0
0
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1
reply
669
views
Dispersion shrinkage in DESeq2: LOESS instead of negative binomial based GLM?
deseq2 RNA-Seq
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
5
votes
6
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1.9k
views
is our edgeR code doing what we think it does?
edger differential expression rna-seq
updated 6.2 years ago by ▴ 900 • written 6.2 years ago by ▴ 10
2
votes
3
replies
1.6k
views
Design for introducing batch effect in DESeq2
deseq2 combat batch effect rna-seq edger
updated 6.2 years ago by ★ 1.4k • written 6.2 years ago by ▴ 80
0
votes
2
replies
1.8k
views
How an index is built for each gene set collections using buildCustomIdx() indexing function of EGSEA package?
EGSEA edgeR biomaRt limma RNA-seq
6.2 years ago fgol ▴ 10
1
vote
4
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1.6k
views
gene Isoforms quantification using RNA-seq data
gene isoform quantification rna-seq
updated 6.2 years ago by ★ 1.4k • written 6.2 years ago by • 0
1
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1
reply
1.3k
views
How to perform RNA-seq with such MDS plot?
limma batch effect rna-seq
updated 6.2 years ago by ★ 1.4k • written 6.2 years ago by • 0
2
votes
7
replies
2.9k
views
RNA-seq with Salmon and tximport
RNA-seq Salmon tximport
updated 6.2 years ago by 68k • written 6.2 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 18 months ago by • 0 • written 6.2 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
6.4 years ago • updated 6.3 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
6.3 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 6.3 years ago by 43k • written 6.3 years ago by ▴ 20
5
votes
3
replies
1.6k
views
DESeq2 with multiple treatments but no replicates
deseq2 rna-seq
updated 6.3 years ago by 43k • written 6.3 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 6.3 years ago by 16k • written 6.3 years ago by ▴ 90
0
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2
replies
1.5k
views
Problem in featureCounts file.
rna-seq featureCounts SubRead
updated 6.3 years ago by ★ 3.6k • written 6.3 years ago by • 0
2
votes
3
replies
2.2k
views
RNAseq and heatmap
deseq2 RNA-seq Heatmap
updated 6.3 years ago by 43k • written 6.3 years ago by ▴ 10
418 results • Page 3 of 9
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The Bioconductor version must be compatible with the R version. Bioconductor version 3.18 is compatible with R version 4.3. The Dockerfile …
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Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Identifying differentially expressed genes in individual samples from a large co
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