Showing : Rnaseq • reset
5
votes
2
replies
2.2k
views
DecideTest vs topTAGs in edgeR
RNAseq StatisticalMethod edgeR
updated 2.1 years ago by 53k • written 2.1 years ago by ▴ 10
0
votes
6
replies
2.3k
views
DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
2.1 years ago erika.maldonado-rosado • 0
0
votes
0
replies
752
views
is Dada2 biased toward a particular sequence ?
virology dada2 amplican Sequencing RNASeq
2.1 years ago Sara • 0
0
votes
2
replies
1.1k
views
Will DESeq2 be appropriate tool for analysis?
RNASeq DESeq2
2.2 years ago • updated 2.1 years ago Karthik • 0
0
votes
0
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742
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Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
2.2 years ago Florian • 0
0
votes
0
replies
1.0k
views
Pysam pileup and Rsamtools pileup output discrepancy
Pysam pileup Rsamtools RNASeq
2.2 years ago Xinqi • 0
0
votes
0
replies
890
views
Using DADA2 for finding viral sequence variants
VariantDetection dada2 RNASeq
2.2 years ago Sara • 0
1
vote
1
reply
1.0k
views
Multiple comparison using DESeq2
RNASeqData RNASeq DESeq2
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
1
vote
7
replies
1.8k
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 2.0 years ago by 53k • written 2.2 years ago by • 0
0
votes
2
replies
872
views
Issues with ddseq2 for treatment response factoring in different KO clones
Clonality RNASeq DESeq2
updated 2.2 years ago by ★ 1.4k • written 2.2 years ago by • 0
0
votes
1
reply
1.1k
views
Comparing RNASeq data from multiple studies
RNASeqData RnaSeqSampleSize RNASeqPower RNASeq
updated 2.2 years ago by ▴ 780 • written 2.2 years ago by • 0
3
votes
5
replies
2.2k
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 2.2 years ago by ★ 5.0k • written 2.3 years ago by • 0
1
vote
1
reply
931
views
bulk RNA-Seq batch correction
RNASeqData rnaseqcomp RNASeq
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by • 0
0
votes
1
reply
862
views
DESeq design and contrast with multiple factors
RNASeq DESeq2
updated 2.3 years ago by 43k • written 2.3 years ago by • 0
1
vote
6
replies
3.5k
views
Time-series RNA-seq analysis using DESeq2
time-series DESeq2 RNASeq timecoursedata TimeCourse
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by • 0
6
votes
7
replies
1.5k
views
Adding a group of samples reduces DEGs in other groups
RNASeq limma
updated 2.4 years ago by 53k • written 2.4 years ago by ▴ 10
0
votes
1
reply
5.1k
views
Is it proper to compare two WGCNA matrixes if they were raised to different power (soft threshold)?
Network cluster WGCNA RNASeq
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
2
votes
1
reply
1.2k
views
Grouping DEGs yields varying results
RNASeq limma
updated 2.4 years ago by 53k • written 2.4 years ago by ▴ 10
2
votes
5
replies
2.1k
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R edgeR RNASeq
2.4 years ago mohammedtoufiq91 ▴ 10
0
votes
2
replies
1.3k
views
Correct DESeq2 design for tumoral stage differences in tumoral and matched-normal samples
DifferentialExpression RNASeq DESeq2
2.4 years ago Matteo • 0
4
votes
2
replies
3.3k
views
Gene set analysis: GSVA, Z-Score, and fold-changes
GSVA RNASeq limma
updated 2.4 years ago by 53k • written 2.4 years ago by ▴ 10
0
votes
3
replies
1.7k
views
Multiple Testing When Using Multiple Contrasts/Comparisons in DESEQ2
MultipleComparison DESeq2 Genetics contrasts RNASeq
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
3
votes
11
replies
4.9k
views
Adjusting for baseline when having longitudinal data, mixed model and no treatment
RNAseq mixedmodels baselineadjustement limma
2.6 years ago • updated 2.5 years ago Anna ▴ 20
2
votes
9
replies
7.0k
views
how to control age and gender effect in expression data using DESeq2
deseq2 rnaseq mirna-seq differential gene expression
written 7.8 years ago by ▴ 10
0
votes
1
reply
885
views
CI for logCPM (fitted values)
RNAseq edgeR
updated 2.6 years ago by 53k • written 2.6 years ago by ▴ 10
3
votes
4
replies
1.1k
views
Anova table edgeR limma
limma RNASeq edgeR
2.6 years ago KATHERINE CHUERE NUNES • 0
1
vote
2
replies
1.1k
views
Obtention of the binomial transformed count table with edgeR
DESeq2 edgeR RNASeq DifferentialExpression
updated 2.6 years ago by 53k • written 2.6 years ago by • 0
0
votes
3
replies
1.4k
views
Account for heteroscedasticity when fitting gene expression data
RNAseq
updated 2.6 years ago by 43k • written 2.6 years ago by • 0
1
vote
3
replies
1.6k
views
Is it okay to increase filtering to get more significant Adjusted P Values for DEGs found using Limma?
RNASeqPower edgeR DifferentialExpression limma RNASeq
updated 2.6 years ago by 53k • written 2.6 years ago by • 0
0
votes
2
replies
2.5k
views
model matrix not full rank
DESeq2 RNASeq
updated 2.6 years ago by • 0 • written 2.6 years ago by • 0
0
votes
1
reply
1.1k
views
What is the correct way to split genex_high and genex_low groups for DE analysis?
DESeq2 RNASeq
updated 2.6 years ago by 43k • written 2.7 years ago by • 0
2
votes
3
replies
870
views
RNA seq with edgeR with several factors
RNAseq factors
2.6 years ago Nathalie ▴ 20
0
votes
3
replies
1.3k
views
edgeR DEGs multilevel
edgeR RNASeq DifferentialRegulation
updated 2.6 years ago by 53k • written 2.6 years ago by • 0
8
votes
10
replies
17k
views
GSEA preranked analysis downstream of DEseq2
deseq2 gsea rnaseq
updated 7 months ago by ★ 5.0k • written 9.4 years ago by ▴ 20
0
votes
4
replies
1.8k
views
Combine RNA-seq
BatchEffect R rnaseq
updated 2.6 years ago by ★ 1.4k • written 2.6 years ago by • 0
1
vote
1
reply
730
views
Using R to measure differential gene expression of one gene due to different treatments using RNASeq counts
DESeq2 edgeR RNAseq
updated 2.6 years ago by 53k • written 2.6 years ago by • 0
3
votes
12
replies
3.0k
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 2.6 years ago by 43k • written 2.7 years ago by ▴ 10
0
votes
1
reply
770
views
Sample expression calculation in rna seq
Rnaseq
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by • 0
1
vote
1
reply
923
views
Can I run deseq2 on two separate experiments at once?
rnaseq deseq2
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by • 0
0
votes
0
replies
979
views
WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome RNAseq WGCNA
2.7 years ago Levi • 0
4
votes
8
replies
6.2k
views
Interpreting ellipses in PCAtools for bulk RNAseq
ellipse RNAseq PCAtools
updated 2.7 years ago by • 0 • written 4.6 years ago by • 0
1
vote
2
replies
1.0k
views
RNA-Seq normalization of pre and post treatment groups
Normalization RNASeq
written 2.7 years ago by • 0
2
votes
4
replies
1.5k
views
limma with or without intercept gives different results
limma rnaseq
2.7 years ago Sydney • 0
1
vote
2
replies
1.8k
views
RUVSeq and DESeq2 -- all variables in design formula must be columns in colData
DESeq2 RNAseq RUVSeq
2.7 years ago garbuzov • 0
0
votes
2
replies
1.2k
views
Compare and filter three BAM files
RNAseq 10X
2.7 years ago wt215 • 0
0
votes
5
replies
1.7k
views
hill-shaped p-value distributions using EdgeR
edgeR p-valuedistribution RNAseq hill-shaped
updated 2.7 years ago by 53k • written 2.7 years ago by • 0
5
votes
7
replies
1.7k
views
different number of DEG because of outliers
DESeq2 RNASeq
updated 23 months ago by 53k • written 2.7 years ago by • 0
0
votes
2
replies
1.6k
views
GO analysis in R vs website
GO RNASeq
2.7 years ago Nitro • 0
1
vote
4
replies
1.3k
views
Repeated Measures-Cross Over Study for RNAseq data using variancePartition::dream
RNAseq variancePartition edgeR dream
2.8 years ago DH • 0
1
vote
0
replies
1.3k
views
Job: Seeking collaborator/contractor (paid) for Bioconductor package development
RNASeq JobPosting
2.8 years ago Jamie Walters ▴ 10
1,410 results • Page 3 of 29
Recent ...
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Comment: Question about RE-agnostic mode for intact Hi-C and Micro-C normalization(HiCDCP by TikTsoksocissalpc • 0
Normalizing complex datasets like Hi C can be challenging, much like setting up a PC for optimal gaming performance. Just as careful tuning…
Comment: p.adjust BH Question by TikTsoksocissalpc • 0
Thanks for sharing your question about RMA limma analysis While working on your experiment, it s always helpful to have some background mu…
Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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