Showing : rna-seq • reset
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565
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To count or not to count multi-overlapping reads?
RNA-Seq featureCounts Rsubread
updated 4 weeks ago by 52k • written 5 weeks ago by ▴ 80
5
votes
3
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27k
views
DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 6.2 years ago by ▴ 30
1
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6
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1.2k
views
Volcano plot has many values around zero
RNA-seq DESeq2 volcanoplot
updated 4 months ago by 43k • written 4 months ago by ▴ 10
0
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2
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427
views
RNA-Seq p value range variation
DESeq2 pvalue RNA-Seq
5 months ago paul.meraner • 0
0
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0
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332
views
WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis genomes RNA-Seq co-expression wgcna
6 months ago Fernanda • 0
1
vote
3
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715
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Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 9 months ago by 68k • written 9 months ago by ▴ 50
2
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4
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808
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 10 months ago by 43k • written 10 months ago by • 0
1
vote
2
replies
779
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
10 months ago Dylan.Sheerin • 0
2
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6
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1.5k
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 20 days ago by • 0 • written 10 months ago by • 0
3
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3
replies
1.3k
views
permutation test in edgeR
rna-seq edgeR
updated 11 months ago by 52k • written 11 months ago by • 0
0
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1
reply
1.2k
views
Human genes correlation to Bacterial genes
correlation pearsoncorrelation rna-seq differential gene expression
updated 15 months ago by ★ 4.7k • written 6.9 years ago by • 0
0
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2
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590
views
WGCNA less samples
RNA-Seq WGCNA Worms
16 months ago davca • 0
0
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4
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1.2k
views
DESeq2 : standardising variation between treatments
RNA-seq DESeq2
17 months ago ar14g12 • 0
0
votes
2
replies
4.4k
views
Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
written 4.7 years ago by ▴ 80
2
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3
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4.0k
views
TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 18 months ago by 52k • written 18 months ago by • 0
0
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3
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1.1k
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RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 18 months ago by ★ 1.9k • written 18 months ago by • 0
3
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4
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1.5k
views
lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
19 months ago Eva ▴ 10
0
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3
replies
997
views
Fishpond with unbalanced dataset
rna-seq salmon fishpond swish
updated 21 months ago by 43k • written 21 months ago by • 0
5
votes
7
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1.8k
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering RNA-Seq CPM edgeR filterByExpr
updated 22 months ago by 52k • written 22 months ago by ▴ 10
0
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3
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1.1k
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 22 months ago by 68k • written 22 months ago by • 0
0
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3
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1.2k
views
Why is RNA-Seq library size not constant among samples?
RNA-Seq sequencer library_size sequency_depth multiplexing offtopic
updated 22 months ago by 68k • written 22 months ago by • 0
1
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1
reply
2.7k
views
FPKM t-test vs DEseq2
DESeq2 statistics rna-seq
updated 23 months ago by ★ 4.7k • written 23 months ago by ▴ 10
0
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1
reply
1.2k
views
Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq Read10X_h5 atac modalities
updated 24 months ago by 68k • written 24 months ago by • 0
2
votes
2
replies
1.1k
views
Multifactorial Design for DESEQ2
DESeq2 rna-seq
updated 24 months ago by ★ 4.7k • written 24 months ago by • 0
0
votes
1
reply
929
views
Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
2.1 years ago Jenny Drnevich ★ 2.0k
0
votes
1
reply
1.1k
views
Error in DESeqDataSetFromHTSeqCount
DESeq2 RNA-seq HTseq DESeqDataSetFromHTSeqCount
updated 2.3 years ago by 43k • written 2.3 years ago by • 0
5
votes
9
replies
2.5k
views
GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
2.7 years ago • updated 2.6 years ago Yang Shi ▴ 10
2
votes
2
replies
1.6k
views
How to judge DEG analysis of these samples could be done by using limma::voom
limma Clustering voom RNA-Seq
2.7 years ago Yang Shi ▴ 10
0
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0
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1.1k
views
Job: Computational Biology Contractor - Chinook Therapeutics
Patient_stratification Multi-omics RNA-seq Kidney_Disease
2.7 years ago eolson • 0
2
votes
2
replies
1.4k
views
How to deal with stronger effect by donor than treatment
MDS RNA-Seq
updated 2.7 years ago by 52k • written 2.7 years ago by • 0
0
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2
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3.6k
views
Incorporating spike-ins to rna-seq analysis
Spike-in RNASeqR DESeq2 Normalization rna-seq
updated 18 months ago by • 0 • written 2.9 years ago by • 0
3
votes
3
replies
4.3k
views
Using PEER to identify hidden confounders in RNA-seq data (not working)
PEER RNA-seq differential expression hidden confounders
updated 3.0 years ago by ▴ 30 • written 6.2 years ago by ▴ 40
5
votes
5
replies
2.2k
views
First principal component variance stabilised RNA-seq data correlates with total read counts per sample / library concentration
RNA-seq PCA control DESeq2 Quality
3.1 years ago • updated 2.9 years ago 9906201a ▴ 20
1
vote
5
replies
2.9k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
3.1 years ago Lucy ▴ 60
1
vote
3
replies
1.9k
views
Two Genotypes Four Treatments RNA-seq Analysis
salmon rna-seq swish bootstrap fishpond
updated 3.1 years ago by 43k • written 3.1 years ago by • 0
0
votes
5
replies
5.2k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 3.2 years ago by ★ 4.7k • written 4.0 years ago by • 0
0
votes
1
reply
1.2k
views
First time Statistical Analysis of RNA-seq
edgeR RNA-Seq log2 foldchange q_value
updated 3.2 years ago by 52k • written 3.2 years ago by • 0
1
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1
reply
3.5k
views
create S-plots with ropls package
s-plot ropls opls-da rna-seq
updated 3.6 years ago by ▴ 10 • written 4.7 years ago by ▴ 10
0
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5
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1.7k
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
3.6 years ago bioinformatic_trainee ▴ 10
0
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0
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1.2k
views
Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
3.7 years ago lianov • 0
0
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1
reply
1.3k
views
Interaction using a single factor model DESeq2
synergy DESeq2 RNA-seq contrast
3.7 years ago • updated 3.6 years ago slcno • 0
3
votes
5
replies
3.7k
views
Negative binomial fitting DESeq2
DESeq2 RNA-seq
updated 3.8 years ago by 43k • written 3.8 years ago by ▴ 60
0
votes
1
reply
2.6k
views
Doing differential expression using FPKM , samples don't have replication
dge fpkm rna-seq
updated 3.8 years ago by ★ 4.0k • written 3.8 years ago by • 0
2
votes
3
replies
1.6k
views
Differential expression error in edgeR - maybe from design matrix?
design edgeR matrix RNA-seq MDplot
updated 3.8 years ago by 52k • written 3.8 years ago by • 0
1
vote
1
reply
2.1k
views
Correlation analyses on TCGA data
RNA-seq Normalization edgeR recount3
updated 3.8 years ago by ★ 1.1k • written 3.8 years ago by ▴ 20
3
votes
4
replies
1.4k
views
need help regarding differential expression analysis
rna-seq
updated 3.8 years ago by ★ 4.0k • written 3.8 years ago by ▴ 20
0
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0
replies
1.2k
views
Job: Computational Biologist, Blood Research Institute, Versiti, Wauwatosa, Wisconsin, USA
RNA-seq Job Single-Cell
3.8 years ago rbrns • 0
1
vote
4
replies
4.7k
views
NA values of count matrix in class DESeqDataSet
rna-seq recount
updated 3.9 years ago by ★ 1.1k • written 7.5 years ago by • 0
3
votes
4
replies
1.8k
views
Pipeline for an Anova-like analysis in edgeR
edgeR anova rna-seq
3.9 years ago Antonio M. • 0
1
vote
2
replies
1.4k
views
multifactorial design matrix
designmatrix RNA-seq limma
updated 4.0 years ago by 52k • written 4.0 years ago by ▴ 20
50 results • Page 1 of 1
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Replies
Comment: DiffBind custom normalization factor by Abbie • 0
Hello! Thanks so much for adding dba.normalize and all the documentation in the manual! I'm hoping I can ask a follow-up question here. I…
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2? by James W. MacDonald 68k
All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…
Comment: Using TPM from tximport of Salmon output for singscore by Kent • 0
Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…
Comment: Using TPM from tximport of Salmon output for singscore by Michael Love 43k
For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…
Comment: DESeq2 model - How to test case/control time course model when taking account wi by Michael Love 43k
I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …
Votes
clusterProfiler-GO enrichment Error
A: Machine learning in R book
Data preparation and Machine learning on time course RNAseq data
Data preparation and Machine learning on time course RNAseq data
Answer: Use of org.Rn.eg.db with GRCr8 reference genome
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