Showing : RNA-SEQ • reset
5
votes
7
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274
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Question about setting threshold using filtering by expression on genes in edgeR
filtering RNA-Seq CPM edgeR filterByExpr
updated 9 days ago by 47k • written 9 days ago by ▴ 10
0
votes
3
replies
201
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 24 days ago by 63k • written 25 days ago by • 0
0
votes
3
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231
views
Why is RNA-Seq library size not constant among samples?
RNA-Seq sequencer library_size sequency_depth multiplexing offtopic
updated 24 days ago by 63k • written 25 days ago by • 0
1
vote
1
reply
177
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
140
views
Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq Read10X_h5 atac modalities
updated 9 weeks ago by 63k • written 9 weeks ago by • 0
2
votes
2
replies
205
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
159
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
288
views
Error in DESeqDataSetFromHTSeqCount
DESeq2 RNA-seq HTseq DESeqDataSetFromHTSeqCount
updated 6 months ago by 40k • written 6 months ago by • 0
5
votes
9
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923
views
GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
10 months ago Yang Shi ▴ 10
2
votes
2
replies
506
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
replies
447
views
Job: Computational Biology Contractor - Chinook Therapeutics
Patient_stratification Multi-omics RNA-seq Kidney_Disease
10 months ago eolson • 0
2
votes
2
replies
411
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 13 months ago by 40k • written 13 months ago by • 0
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
1.0k
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
780
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
1
reply
512
views
First time Statistical Analysis of RNA-seq
edgeR RNA-Seq log2 foldchange q_value
updated 16 months ago by 47k • written 16 months ago by • 0
0
votes
5
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678
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
votes
0
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493
views
Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
22 months ago lianov • 0
0
votes
1
reply
514
views
Interaction using a single factor model DESeq2
synergy DESeq2 RNA-seq contrast
22 months ago • updated 21 months ago slcno • 0
3
votes
5
replies
1.6k
views
Negative binomial fitting DESeq2
DESeq2 RNA-seq
updated 23 months ago by 40k • written 23 months ago by ▴ 60
0
votes
1
reply
735
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
782
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
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
replies
602
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
replies
585
views
Job: Computational Biologist, Blood Research Institute, Versiti, Wauwatosa, Wisconsin, USA
RNA-seq Job Single-Cell
2.0 years ago rbrns • 0
3
votes
4
replies
877
views
Pipeline for an Anova-like analysis in edgeR
edgeR anova rna-seq
2.1 years ago Antonio M. • 0
1
vote
2
replies
699
views
multifactorial design matrix
designmatrix RNA-seq limma
updated 2.2 years ago by 47k • written 2.2 years ago by ▴ 20
0
votes
5
replies
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
1
vote
7
replies
929
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
543
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
replies
590
views
Normalization for WGCNA on two organisms (virus-host)
RNA-Seq DESeq2 WGCNA Normalization
2.4 years ago wrzl • 0
0
votes
1
reply
640
views
Limma/Voom Normalized Counts
limma RNA-seq
updated 2.5 years ago by 47k • written 2.5 years ago by • 0
3
votes
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
2
replies
854
views
RNA-seq read simulation for benchmarking differential expression/splicing variance
polyester simulation RNA-seq syntheticdata
updated 2.5 years ago by 47k • written 2.5 years ago by ▴ 60
0
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2
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774
views
Pathway analysis using GAGE returns all NA values
gage rna-seq pathwayanalysis
updated 23 days ago by • 0 • written 2.6 years ago by • 0
3
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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
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3
replies
695
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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976
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
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609
views
Job: Bioinformatics Developer / Computational Biologist
bioinformatics rna-seq shiny apps R algorithm development Job
2.6 years ago mmartin ▴ 20
0
votes
3
replies
879
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
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0
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540
views
circRNAprofiler - miRNA binding sites
circRNA RNA-seq circRNAprofiler
2.6 years ago Terra • 0
0
votes
0
replies
867
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
772
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
replies
824
views
Pathway analysis of bacterial RNA-seq data
annotation rna-seq pathway analysis
2.7 years ago microPhD • 0
3
votes
1
reply
587
views
How do you create a targets dataframe in edgeR?
edgeR RNA-SEQ
updated 2.7 years ago by 63k • written 2.7 years ago by • 0
5
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6
replies
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
1
vote
1
reply
768
views
Having issues mapping gene Ids during ReportingTools::publish() from Bioconductor.
ReportingTools RNA-Seq RMarkdown
updated 2.7 years ago by 63k • written 2.8 years ago by ▴ 20
1
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4
replies
1.2k
views
Issues with DESeq2 LRT for time-course experiment
rna-seq R DESeq2 LRT
updated 2.8 years ago by 3.8k • written 2.8 years ago by ▴ 10
0
votes
1
reply
579
views
dupRadar: low % of duplicates for 150bp PE RNAseq
dupRadar 150bp RNA-seq
updated 2.8 years ago by ▴ 80 • written 2.8 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Diffbind "No genome detected" by kyliecode • 0
Hi James, Thanks for your reply! For the blacklist, I just used the one provided by DiffBind, which is "DBA_BLACKLIST_MM10". For the grey…
Answer: DESeq2 on multilevel design variable by ATpoint ★ 2.9k
You can make your life simply and use a contrast for each, for example: ```r library(DESeq2) dds <- makeExampleDESeqDataSet() diagnosis <…
Answer: Diffbind "No genome detected" by James W. MacDonald 63k
You can specify the greylist in the same manner as the blacklist, which should fix your problem.
Answer: Generate false reads for testing by James W. MacDonald 63k
https://www.bioconductor.org/packages/release/bioc/html/polyester.html
Comment: Adjusting for baseline when having longitudinal data, mixed model and no treat by Anna ▴ 20
Yes. But still I prefer using the covariance matrix over fixed effects for power issues. Or at least I wanted to use it as such before our …
Votes
Answer: Annotation with org.Hs.eg.db Genome Build 38
Comment: Adjusting for baseline when having longitudinal data, mixed model and no treat
A: overlap GRangesList and vcf
A: Ranges from a fasta file
Answer: NA transcript values in my Txdb
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