Showing : RNA-SEQ • reset
5
votes
7
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283
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Question about setting threshold using filtering by expression on genes in edgeR
filtering RNA-Seq CPM edgeR filterByExpr
updated 12 days ago by 47k • written 12 days ago by ▴ 10
0
votes
3
replies
203
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 27 days ago by 63k • written 27 days ago by • 0
0
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3
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235
views
Why is RNA-Seq library size not constant among samples?
RNA-Seq sequencer library_size sequency_depth multiplexing offtopic
updated 27 days ago by 63k • written 27 days ago by • 0
1
vote
1
reply
183
views
FPKM t-test vs DEseq2
DESeq2 statistics rna-seq
updated 7 weeks ago by ★ 2.9k • written 7 weeks ago by • 0
0
votes
1
reply
143
views
Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq Read10X_h5 atac modalities
updated 10 weeks ago by 63k • written 10 weeks ago by • 0
2
votes
2
replies
207
views
Multifactorial Design for DESEQ2
DESeq2 rna-seq
updated 10 weeks ago by ★ 2.9k • written 10 weeks ago by • 0
0
votes
1
reply
161
views
Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
3 months ago Jenny Drnevich ★ 2.0k
0
votes
1
reply
291
views
Error in DESeqDataSetFromHTSeqCount
DESeq2 RNA-seq HTseq DESeqDataSetFromHTSeqCount
updated 6 months ago by 40k • written 6 months ago by • 0
5
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9
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924
views
GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
10 months ago Yang Shi ▴ 10
2
votes
2
replies
512
views
How to judge DEG analysis of these samples could be done by using limma::voom
limma Clustering voom RNA-Seq
10 months ago Yang Shi ▴ 10
0
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0
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453
views
Job: Computational Biology Contractor - Chinook Therapeutics
Patient_stratification Multi-omics RNA-seq Kidney_Disease
10 months ago eolson • 0
2
votes
2
replies
415
views
How to deal with stronger effect by donor than treatment
MDS RNA-Seq
updated 10 months ago by 47k • written 10 months ago by • 0
0
votes
1
reply
1.1k
views
Incorporating spike-ins to rna-seq analysis
Spike-in RNASeqR DESeq2 Normalization rna-seq
updated 14 months ago by 40k • written 14 months ago by • 0
2
votes
3
replies
2.3k
views
Using PEER to identify hidden confounders in RNA-seq data (not working)
PEER RNA-seq differential expression hidden confounders
updated 14 months ago by ▴ 20 • written 4.4 years ago by ▴ 30
5
votes
5
replies
970
views
First principal component variance stabilised RNA-seq data correlates with total read counts per sample / library concentration
RNA-seq PCA control DESeq2 Quality
15 months ago • updated 13 months ago 9906201a ▴ 20
1
vote
5
replies
1.1k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
16 months ago • updated 15 months ago Lucy ▴ 60
1
vote
3
replies
783
views
Two Genotypes Four Treatments RNA-seq Analysis
salmon rna-seq swish bootstrap fishpond
updated 15 months ago by 40k • written 16 months ago by • 0
0
votes
5
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2.0k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 16 months ago by ★ 2.9k • written 2.2 years ago by • 0
0
votes
1
reply
513
views
First time Statistical Analysis of RNA-seq
edgeR RNA-Seq log2 foldchange q_value
updated 17 months ago by 47k • written 17 months ago by • 0
1
vote
1
reply
1.7k
views
create S-plots with ropls package
s-plot ropls opls-da rna-seq
updated 21 months ago by ▴ 10 • written 2.9 years ago by ▴ 10
0
votes
5
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681
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
22 months ago bioinformatic_trainee ▴ 10
0
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0
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495
views
Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
22 months ago lianov • 0
0
votes
1
reply
516
views
Interaction using a single factor model DESeq2
synergy DESeq2 RNA-seq contrast
22 months ago slcno • 0
3
votes
5
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1.6k
views
Negative binomial fitting DESeq2
DESeq2 RNA-seq
updated 24 months ago by 40k • written 24 months ago by ▴ 60
0
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1
reply
739
views
Doing differential expression using FPKM , samples don't have replication
dge fpkm rna-seq
updated 2.0 years ago by 3.8k • written 2.0 years ago by • 0
2
votes
3
replies
783
views
Differential expression error in edgeR - maybe from design matrix?
design edgeR matrix RNA-seq MDplot
updated 2.0 years ago by 47k • written 2.0 years ago by • 0
5
votes
2
replies
16k
views
DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
updated 16 months ago by • 0 • written 4.4 years ago by ▴ 30
1
vote
1
reply
1.1k
views
Correlation analyses on TCGA data
RNA-seq Normalization edgeR recount3
updated 2.0 years ago by ★ 1.0k • written 2.0 years ago by ▴ 20
3
votes
4
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603
views
need help regarding differential expression analysis
rna-seq
updated 2.0 years ago by 3.8k • written 2.0 years ago by ▴ 20
0
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0
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589
views
Job: Computational Biologist, Blood Research Institute, Versiti, Wauwatosa, Wisconsin, USA
RNA-seq Job Single-Cell
2.1 years ago rbrns • 0
1
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4
replies
2.8k
views
NA values of count matrix in class DESeqDataSet
rna-seq recount
updated 2.1 years ago by ★ 1.0k • written 5.7 years ago by • 0
3
votes
4
replies
880
views
Pipeline for an Anova-like analysis in edgeR
edgeR anova rna-seq
2.1 years ago Antonio M. • 0
1
vote
2
replies
700
views
multifactorial design matrix
designmatrix RNA-seq limma
updated 2.2 years ago by 47k • written 2.2 years ago by ▴ 20
1
vote
7
replies
932
views
how to make a contrast of uniquely DE genes
edgeR limma RNA-seq DEGseq
2.2 years ago decppced • 0
1
vote
3
replies
547
views
Questions regarding DESeq2 experimental setup and lfcShrink
DESeq2 RNA-seq
updated 2.2 years ago by 40k • written 2.2 years ago by • 0
0
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0
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593
views
Normalization for WGCNA on two organisms (virus-host)
RNA-Seq DESeq2 WGCNA Normalization
2.4 years ago wrzl • 0
3
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9
replies
1.6k
views
summarizeToGene from tximeta: not all 'rnames' found or unique.
RNA-seq tximeta
2.5 years ago Pufall, Miles A ▴ 30
0
votes
1
reply
642
views
Limma/Voom Normalized Counts
limma RNA-seq
updated 2.5 years ago by 47k • written 2.5 years ago by • 0
0
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2
replies
859
views
RNA-seq read simulation for benchmarking differential expression/splicing variance
polyester simulation RNA-seq syntheticdata
updated 2.6 years ago by 47k • written 2.6 years ago by ▴ 60
0
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2
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777
views
Pathway analysis using GAGE returns all NA values
gage rna-seq pathwayanalysis
updated 26 days ago by • 0 • written 2.6 years ago by • 0
3
votes
6
replies
2.0k
views
DESeq2: When to split multiple group samples for 'more' accurate sizefactors, dispersions etc.
Dispersion RNA-seq DESeq2 Multiple-group
updated 2.3 years ago by 40k • written 2.6 years ago by ▴ 10
0
votes
3
replies
880
views
GSVA on gene sets with 2 genes
GSVA gene sets RNA-seq
updated 2.6 years ago by ★ 3.0k • written 2.6 years ago by ▴ 60
0
votes
3
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699
views
Weird set of samples in plant gene atlas study that appear over-corrected after DESeq2 normalization
RNA-Seq DESeq2
updated 2.6 years ago by 40k • written 2.6 years ago by • 0
0
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0
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979
views
how to find consensus modules between 2 datasets by different platform through WGCNA
consensusmodule microarray RNA-seq WGCNA
2.6 years ago modarzi ▴ 10
0
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0
replies
610
views
Job: Bioinformatics Developer / Computational Biologist
bioinformatics rna-seq shiny apps R algorithm development Job
2.6 years ago mmartin ▴ 20
0
votes
0
replies
540
views
circRNAprofiler - miRNA binding sites
circRNA RNA-seq circRNAprofiler
2.7 years ago • updated 2.6 years ago Terra • 0
0
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0
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868
views
HISAT2/StringTie/Ballgown for Novel Transcript Isoform Differential Expression
isoform RNA-seq hisat2 stringtie ballgown
2.7 years ago ra711 • 0
3
votes
3
replies
776
views
Problem to understand Interactions at any time
RNA-seq edgeR interactions
updated 2.7 years ago by 47k • written 2.7 years ago by ▴ 10
0
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3
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828
views
Pathway analysis of bacterial RNA-seq data
annotation rna-seq pathway analysis
2.7 years ago microPhD • 0
5
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6
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1.1k
views
RUVseq to remove a library size artefact in a zebrafish brain RNA-seq dataset
RUVSeq RUV RNA-seq
updated 2.7 years ago by 63k • written 2.7 years ago by ▴ 20
50 results • Page 1 of 1
Recent ...
Replies
Comment: DeSEQ 2 Error: some values in assay are negative by James W. MacDonald 63k
In order to back up your assertion that there are no negative values, you should provide evidence. For example ``` any(countData < 0) dds …
Answer: DeSEQ 2 Error: some values in assay are negative by Michael Love 40k
You don't need to remove 0's. What do you get with ``` any(countData < 0) ``` (fixed, typo first time around)
Comment: Interpret plot from DiffBind by Rory Stark ★ 4.9k
See above, you want the sites where `Fold > 0`.
Comment: Interpret plot from DiffBind by Rory Stark ★ 4.9k
That does seem like you have a very high number of open chromatin sites changing. How many are in the consensus matrix? You can see how ma…
Comment: Interpret plot from DiffBind by Rory Stark ★ 4.9k
I can see the confusion here as one color is being used in two different ways. The dark blue/purple color is used for the bars on the left…
Votes
DESeq2 for time-course with nested individuals
Answer: Using PEER to identify hidden confounders in RNA-seq data (not working)
Answer: Using PEER to identify hidden confounders in RNA-seq data (not working)
Answer: P-value histogram of testLinearModel is not uniform
Answer: Interpret plot from DiffBind
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Scholar to Rory Stark ★ 4.9k
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