Showing : RNA-seq • reset
0
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665
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To count or not to count multi-overlapping reads?
RNA-Seq featureCounts Rsubread
updated 3 months ago by 52k • written 3 months ago by ▴ 80
5
votes
3
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28k
views
DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 6.4 years ago by ▴ 30
1
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6
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1.3k
views
Volcano plot has many values around zero
RNA-seq DESeq2 volcanoplot
updated 6 months ago by 43k • written 6 months ago by ▴ 10
0
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2
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500
views
RNA-Seq p value range variation
DESeq2 pvalue RNA-Seq
7 months ago paul.meraner • 0
0
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0
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427
views
WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis genomes RNA-Seq co-expression wgcna
7 months ago Fernanda • 0
1
vote
3
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790
views
Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 11 months ago by 68k • written 11 months ago by ▴ 50
2
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4
replies
884
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 12 months ago by 43k • written 12 months ago by • 0
1
vote
2
replies
845
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
12 months ago Dylan.Sheerin • 0
2
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6
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1.8k
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 11 weeks ago by • 0 • written 12 months ago by • 0
3
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3
replies
1.5k
views
permutation test in edgeR
rna-seq edgeR
updated 13 months ago by 52k • written 13 months ago by • 0
0
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1
reply
1.2k
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Human genes correlation to Bacterial genes
correlation pearsoncorrelation rna-seq differential gene expression
updated 17 months ago by ★ 4.8k • written 7.1 years ago by • 0
0
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2
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641
views
WGCNA less samples
RNA-Seq WGCNA Worms
18 months ago davca • 0
0
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4
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1.3k
views
DESeq2 : standardising variation between treatments
RNA-seq DESeq2
19 months ago ar14g12 • 0
0
votes
2
replies
4.6k
views
Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
written 4.8 years ago by ▴ 80
2
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3
replies
4.5k
views
TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 20 months ago by 52k • written 20 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 20 months ago by ★ 1.9k • written 20 months ago by • 0
3
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4
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1.6k
views
lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
21 months ago Eva ▴ 10
0
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3
replies
1.0k
views
Fishpond with unbalanced dataset
rna-seq salmon fishpond swish
updated 23 months ago by 43k • written 23 months ago by • 0
5
votes
7
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1.9k
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering RNA-Seq CPM edgeR filterByExpr
updated 24 months ago by 52k • written 24 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 2.0 years ago by 68k • written 2.0 years ago by • 0
0
votes
3
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1.3k
views
Why is RNA-Seq library size not constant among samples?
RNA-Seq sequencer library_size sequency_depth multiplexing offtopic
updated 2.0 years ago by 68k • written 2.0 years ago by • 0
1
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1
reply
3.0k
views
FPKM t-test vs DEseq2
DESeq2 statistics rna-seq
updated 2.1 years ago by ★ 4.8k • written 2.1 years ago by ▴ 10
0
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1
reply
1.3k
views
Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq Read10X_h5 atac modalities
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
2
votes
2
replies
1.2k
views
Multifactorial Design for DESEQ2
DESeq2 rna-seq
updated 2.1 years ago by ★ 4.8k • written 2.2 years ago by • 0
0
votes
1
reply
962
views
Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
2.3 years ago Jenny Drnevich ★ 2.0k
0
votes
1
reply
1.1k
views
Error in DESeqDataSetFromHTSeqCount
DESeq2 RNA-seq HTseq DESeqDataSetFromHTSeqCount
updated 2.5 years ago by 43k • written 2.5 years ago by • 0
5
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9
replies
2.7k
views
GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
2.8 years ago Yang Shi ▴ 10
2
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2
replies
1.8k
views
How to judge DEG analysis of these samples could be done by using limma::voom
limma Clustering voom RNA-Seq
2.8 years ago Yang Shi ▴ 10
0
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0
replies
1.2k
views
Job: Computational Biology Contractor - Chinook Therapeutics
Patient_stratification Multi-omics RNA-seq Kidney_Disease
2.8 years ago eolson • 0
2
votes
2
replies
1.5k
views
How to deal with stronger effect by donor than treatment
MDS RNA-Seq
updated 2.8 years ago by 52k • written 2.8 years ago by • 0
0
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2
replies
3.9k
views
Incorporating spike-ins to rna-seq analysis
Spike-in RNASeqR DESeq2 Normalization rna-seq
updated 20 months ago by • 0 • written 3.1 years ago by • 0
3
votes
3
replies
4.4k
views
Using PEER to identify hidden confounders in RNA-seq data (not working)
PEER RNA-seq differential expression hidden confounders
updated 3.2 years ago by ▴ 30 • written 6.3 years ago by ▴ 40
5
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5
replies
2.8k
views
First principal component variance stabilised RNA-seq data correlates with total read counts per sample / library concentration
RNA-seq PCA control DESeq2 Quality
3.2 years ago • updated 3.0 years ago 9906201a ▴ 20
1
vote
5
replies
3.1k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
3.3 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 3.3 years ago by 43k • written 3.3 years ago by • 0
0
votes
5
replies
5.5k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 3.3 years ago by ★ 4.8k • written 4.2 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 3.3 years ago by 52k • written 3.4 years ago by • 0
1
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1
reply
3.7k
views
create S-plots with ropls package
s-plot ropls opls-da rna-seq
updated 3.8 years ago by ▴ 10 • written 4.9 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
3.8 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
3.8 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
3.8 years ago slcno • 0
3
votes
5
replies
4.0k
views
Negative binomial fitting DESeq2
DESeq2 RNA-seq
updated 3.9 years ago by 43k • written 3.9 years ago by ▴ 60
0
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1
reply
2.7k
views
Doing differential expression using FPKM , samples don't have replication
dge fpkm rna-seq
updated 4.0 years ago by ★ 4.0k • written 4.0 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 4.0 years ago by 52k • written 4.0 years ago by • 0
1
vote
1
reply
2.1k
views
Correlation analyses on TCGA data
RNA-seq Normalization edgeR recount3
updated 4.0 years ago by ★ 1.1k • written 4.0 years ago by ▴ 20
3
votes
4
replies
1.5k
views
need help regarding differential expression analysis
rna-seq
updated 4.0 years ago by ★ 4.0k • written 4.0 years ago by ▴ 20
0
votes
0
replies
1.2k
views
Job: Computational Biologist, Blood Research Institute, Versiti, Wauwatosa, Wisconsin, USA
RNA-seq Job Single-Cell
4.0 years ago rbrns • 0
1
vote
4
replies
4.8k
views
NA values of count matrix in class DESeqDataSet
rna-seq recount
updated 4.1 years ago by ★ 1.1k • written 7.6 years ago by • 0
3
votes
4
replies
1.8k
views
Pipeline for an Anova-like analysis in edgeR
edgeR anova rna-seq
4.1 years ago Antonio M. • 0
1
vote
2
replies
1.4k
views
multifactorial design matrix
designmatrix RNA-seq limma
updated 4.1 years ago by 52k • written 4.2 years ago by ▴ 20
50 results • Page 1 of 1
Recent ...
Replies
Comment: Check removeBatchEffect effectiveness by Gordon Smyth 52k
Both of your matrices, `design_batcheffects` and `design_timepoint`, span the intercept term, which will cause a warning about NA coefficie…
Comment: DiffBind - question on the use of filtered or unfiltered input data by sloperun3az • 0
Your essay was beneficial to me, and I found it to be very useful. Thank you for writing it. You give a wealth of knowledge that is not onl…
Comment: compute_fasta_digest does not match Salmon index hash by sloperun3az • 0
The people who are reading your work are not taken into consideration, even though you appear to have a solid understanding of the subject …
Comment: parameters of filterByExpr by Paul Harrison ▴ 110
It might be worth trying limma-voom (or limma-trend) instead of a GLM based method. In our experience these are less prone to this problem.…
Comment: limma::voom vs edgeR::voomLmFit - when to use? by Gordon Smyth 52k
voomLmFit() is in edgeR instead of limma because it needs to call edgeR::glmFit() internally to determine which of the zero observations al…
Votes
Comment: Check removeBatchEffect effectiveness
Answer: Check removeBatchEffect effectiveness
A: what should I do with many zero counts from Salmon quantification
Comment: parameters of filterByExpr
GAlignments Cigar to GRanges
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