Showing : rna-seq • reset
5
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DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 5.9 years ago by ▴ 30
1
vote
6
replies
943
views
Volcano plot has many values around zero
RNA-seq DESeq2 volcanoplot
updated 6 weeks ago by 43k • written 6 weeks ago by ▴ 10
0
votes
2
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296
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RNA-Seq p value range variation
DESeq2 pvalue RNA-Seq
11 weeks ago • updated 10 weeks ago paul.meraner • 0
0
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0
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210
views
WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis genomes RNA-Seq co-expression wgcna
3 months ago Fernanda • 0
1
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3
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574
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Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 6 months ago by 67k • written 6 months ago by ▴ 50
2
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4
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679
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DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 7 months ago by 43k • written 7 months ago by • 0
1
vote
2
replies
643
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
7 months ago Dylan.Sheerin • 0
2
votes
5
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1.0k
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 6 months ago by ★ 4.6k • written 7 months ago by • 0
3
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3
replies
933
views
permutation test in edgeR
rna-seq edgeR
updated 8 months ago by 52k • written 8 months ago by • 0
0
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1
reply
1.1k
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Human genes correlation to Bacterial genes
correlation pearsoncorrelation rna-seq differential gene expression
updated 12 months ago by ★ 4.6k • written 6.7 years ago by • 0
0
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2
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532
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WGCNA less samples
RNA-Seq WGCNA Worms
13 months ago davca • 0
0
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4
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1.1k
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DESeq2 : standardising variation between treatments
RNA-seq DESeq2
14 months ago ar14g12 • 0
0
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2
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4.1k
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Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
written 4.4 years ago by ▴ 80
2
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3
replies
3.4k
views
TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 15 months ago by 52k • written 15 months ago by • 0
0
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3
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983
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RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 15 months ago by ★ 1.9k • written 15 months ago by • 0
3
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4
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1.3k
views
lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
16 months ago Eva ▴ 10
0
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3
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919
views
Fishpond with unbalanced dataset
rna-seq salmon fishpond swish
updated 18 months ago by 43k • written 18 months ago by • 0
5
votes
7
replies
1.6k
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering RNA-Seq CPM edgeR filterByExpr
updated 19 months ago by 52k • written 19 months ago by ▴ 10
0
votes
3
replies
998
views
Is the gene-specific PCR efficiency a serious concern for intrasample comparisons in RNA-Seq?
RNA-Seq normalization PCR_efficiency bias intrasample_comparison
updated 19 months ago by 67k • written 19 months ago by • 0
0
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3
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1.1k
views
Why is RNA-Seq library size not constant among samples?
RNA-Seq sequencer library_size sequency_depth multiplexing offtopic
updated 19 months ago by 67k • written 19 months ago by • 0
1
vote
1
reply
2.3k
views
FPKM t-test vs DEseq2
DESeq2 statistics rna-seq
updated 20 months ago by ★ 4.6k • written 20 months ago by ▴ 10
0
votes
1
reply
1.0k
views
Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq Read10X_h5 atac modalities
updated 21 months ago by 67k • written 21 months ago by • 0
2
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2
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1.0k
views
Multifactorial Design for DESEQ2
DESeq2 rna-seq
updated 21 months ago by ★ 4.6k • written 21 months ago by • 0
0
votes
1
reply
871
views
Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
22 months ago Jenny Drnevich ★ 2.0k
0
votes
1
reply
996
views
Error in DESeqDataSetFromHTSeqCount
DESeq2 RNA-seq HTseq DESeqDataSetFromHTSeqCount
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
5
votes
9
replies
2.4k
views
GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
2.4 years ago Yang Shi ▴ 10
2
votes
2
replies
1.5k
views
How to judge DEG analysis of these samples could be done by using limma::voom
limma Clustering voom RNA-Seq
2.4 years ago Yang Shi ▴ 10
0
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0
replies
1.1k
views
Job: Computational Biology Contractor - Chinook Therapeutics
Patient_stratification Multi-omics RNA-seq Kidney_Disease
2.4 years ago eolson • 0
2
votes
2
replies
1.3k
views
How to deal with stronger effect by donor than treatment
MDS RNA-Seq
updated 2.4 years ago by 52k • written 2.4 years ago by • 0
0
votes
2
replies
3.2k
views
Incorporating spike-ins to rna-seq analysis
Spike-in RNASeqR DESeq2 Normalization rna-seq
updated 15 months ago by • 0 • written 2.7 years ago by • 0
3
votes
3
replies
4.0k
views
Using PEER to identify hidden confounders in RNA-seq data (not working)
PEER RNA-seq differential expression hidden confounders
updated 2.8 years ago by ▴ 30 • written 5.9 years ago by ▴ 40
5
votes
5
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2.1k
views
First principal component variance stabilised RNA-seq data correlates with total read counts per sample / library concentration
RNA-seq PCA control DESeq2 Quality
2.8 years ago • updated 2.6 years ago 9906201a ▴ 20
1
vote
5
replies
2.6k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
2.9 years ago • updated 2.8 years ago Lucy ▴ 60
1
vote
3
replies
1.7k
views
Two Genotypes Four Treatments RNA-seq Analysis
salmon rna-seq swish bootstrap fishpond
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
0
votes
5
replies
4.6k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 2.9 years ago by ★ 4.6k • written 3.7 years ago by • 0
0
votes
1
reply
1.1k
views
First time Statistical Analysis of RNA-seq
edgeR RNA-Seq log2 foldchange q_value
updated 2.9 years ago by 52k • written 2.9 years ago by • 0
1
vote
1
reply
3.3k
views
create S-plots with ropls package
s-plot ropls opls-da rna-seq
updated 3.3 years ago by ▴ 10 • written 4.5 years ago by ▴ 10
0
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5
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1.5k
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DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
3.4 years ago bioinformatic_trainee ▴ 10
0
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0
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1.1k
views
Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
3.4 years ago lianov • 0
0
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1
reply
1.2k
views
Interaction using a single factor model DESeq2
synergy DESeq2 RNA-seq contrast
3.4 years ago slcno • 0
3
votes
5
replies
3.3k
views
Negative binomial fitting DESeq2
DESeq2 RNA-seq
updated 3.5 years ago by 43k • written 3.5 years ago by ▴ 60
0
votes
1
reply
2.3k
views
Doing differential expression using FPKM , samples don't have replication
dge fpkm rna-seq
updated 3.6 years ago by ★ 4.0k • written 3.6 years ago by • 0
2
votes
3
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1.4k
views
Differential expression error in edgeR - maybe from design matrix?
design edgeR matrix RNA-seq MDplot
updated 3.6 years ago by 52k • written 3.6 years ago by • 0
1
vote
1
reply
2.0k
views
Correlation analyses on TCGA data
RNA-seq Normalization edgeR recount3
updated 3.6 years ago by ★ 1.1k • written 3.6 years ago by ▴ 20
3
votes
4
replies
1.3k
views
need help regarding differential expression analysis
rna-seq
updated 3.6 years ago by ★ 4.0k • written 3.6 years ago by ▴ 20
0
votes
0
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1.1k
views
Job: Computational Biologist, Blood Research Institute, Versiti, Wauwatosa, Wisconsin, USA
RNA-seq Job Single-Cell
3.6 years ago rbrns • 0
1
vote
4
replies
4.4k
views
NA values of count matrix in class DESeqDataSet
rna-seq recount
updated 3.7 years ago by ★ 1.1k • written 7.2 years ago by • 0
3
votes
4
replies
1.7k
views
Pipeline for an Anova-like analysis in edgeR
edgeR anova rna-seq
3.7 years ago Antonio M. • 0
1
vote
2
replies
1.3k
views
multifactorial design matrix
designmatrix RNA-seq limma
updated 3.7 years ago by 52k • written 3.7 years ago by ▴ 20
1
vote
7
replies
1.7k
views
how to make a contrast of uniquely DE genes
edgeR limma RNA-seq DEGseq
3.8 years ago decppced • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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