Showing : RNA-Seq • reset
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149
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Error in DESeqDataSetFromHTSeqCount
DESeq2 RNA-seq HTseq DESeqDataSetFromHTSeqCount
updated 10 weeks ago by 39k • written 11 weeks ago by • 0
5
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9
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685
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GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
6 months ago Yang Shi • 0
2
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2
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353
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How to judge DEG analysis of these samples could be done by using limma::voom
limma Clustering voom RNA-Seq
6 months ago Yang Shi • 0
0
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0
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314
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Job: Computational Biology Contractor - Chinook Therapeutics
Patient_stratification Multi-omics RNA-seq Kidney_Disease
6 months ago eolson • 0
2
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2
replies
288
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How to deal with stronger effect by donor than treatment
MDS RNA-Seq
updated 7 months ago by 47k • written 7 months ago by • 0
0
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1
reply
700
views
Incorporating spike-ins to rna-seq analysis
Spike-in RNASeqR DESeq2 Normalization rna-seq
updated 10 months ago by 39k • written 10 months ago by • 0
0
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3
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2.0k
views
Using PEER to identify hidden confounders in RNA-seq data (not working)
PEER RNA-seq differential expression hidden confounders
updated 10 months ago by • 0 • written 4.0 years ago by ▴ 30
5
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5
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737
views
First principal component variance stabilised RNA-seq data correlates with total read counts per sample / library concentration
RNA-seq PCA control DESeq2 Quality
11 months ago • updated 9 months ago 9906201a ▴ 20
1
vote
5
replies
789
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
12 months ago • updated 11 months ago Lucy ▴ 60
1
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3
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610
views
Two Genotypes Four Treatments RNA-seq Analysis
salmon rna-seq swish bootstrap fishpond
updated 12 months ago by 39k • written 12 months ago by • 0
0
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5
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1.6k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 13 months ago by ★ 2.1k • written 22 months ago by • 0
0
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1
reply
402
views
First time Statistical Analysis of RNA-seq
edgeR RNA-Seq log2 foldchange q_value
updated 13 months ago by 47k • written 13 months ago by • 0
1
vote
1
reply
1.4k
views
create S-plots with ropls package
s-plot ropls opls-da rna-seq
updated 18 months ago by ▴ 10 • written 2.6 years ago by ▴ 10
0
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5
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520
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DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
18 months ago bioinformatic_trainee ▴ 10
0
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0
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403
views
Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
18 months ago lianov • 0
0
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1
reply
410
views
Interaction using a single factor model DESeq2
synergy DESeq2 RNA-seq contrast
18 months ago slcno • 0
3
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5
replies
1.3k
views
Negative binomial fitting DESeq2
DESeq2 RNA-seq
updated 20 months ago by 39k • written 20 months ago by ▴ 60
0
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1
reply
549
views
Doing differential expression using FPKM , samples don't have replication
dge fpkm rna-seq
updated 20 months ago by 3.7k • written 20 months ago by • 0
2
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3
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660
views
Differential expression error in edgeR - maybe from design matrix?
design edgeR matrix RNA-seq MDplot
updated 20 months ago by 47k • written 20 months ago by • 0
5
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2
replies
14k
views
DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
updated 12 months ago by • 0 • written 4.1 years ago by ▴ 30
1
vote
1
reply
888
views
Correlation analyses on TCGA data
RNA-seq Normalization edgeR recount3
updated 20 months ago by ★ 1.0k • written 20 months ago by ▴ 10
3
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4
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485
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need help regarding differential expression analysis
rna-seq
updated 20 months ago by 3.7k • written 20 months ago by ▴ 20
0
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0
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446
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Job: Computational Biologist, Blood Research Institute, Versiti, Wauwatosa, Wisconsin, USA
RNA-seq Job Single-Cell
21 months ago rbrns • 0
1
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4
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2.4k
views
NA values of count matrix in class DESeqDataSet
rna-seq recount
updated 21 months ago by ★ 1.0k • written 5.4 years ago by • 0
3
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4
replies
726
views
Pipeline for an Anova-like analysis in edgeR
edgeR anova rna-seq
21 months ago Antonio M. • 0
1
vote
2
replies
592
views
multifactorial design matrix
designmatrix RNA-seq limma
updated 22 months ago by 47k • written 22 months ago by ▴ 20
1
vote
7
replies
782
views
how to make a contrast of uniquely DE genes
edgeR limma RNA-seq DEGseq
23 months ago decppced • 0
1
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3
replies
444
views
Questions regarding DESeq2 experimental setup and lfcShrink
DESeq2 RNA-seq
updated 23 months ago by 39k • written 23 months ago by • 0
0
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0
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508
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Normalization for WGCNA on two organisms (virus-host)
RNA-Seq DESeq2 WGCNA Normalization
2.0 years ago wrzl • 0
3
votes
9
replies
1.3k
views
summarizeToGene from tximeta: not all 'rnames' found or unique.
RNA-seq tximeta
2.2 years ago • updated 2.1 years ago Pufall, Miles A ▴ 30
0
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1
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533
views
Limma/Voom Normalized Counts
limma RNA-seq
updated 2.2 years ago by 47k • written 2.2 years ago by • 0
0
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2
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663
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RNA-seq read simulation for benchmarking differential expression/splicing variance
polyester simulation RNA-seq syntheticdata
updated 2.2 years ago by 47k • written 2.2 years ago by ▴ 60
0
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1
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587
views
Pathway analysis using GAGE returns all NA values
gage rna-seq pathwayanalysis
updated 2.3 years ago by 3.7k • written 2.3 years ago by • 0
2
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6
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1.7k
views
DESeq2: When to split multiple group samples for 'more' accurate sizefactors, dispersions etc.
Dispersion RNA-seq DESeq2 Multiple-group
updated 24 months ago by 39k • written 2.3 years ago by • 0
0
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3
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744
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GSVA on gene sets with 2 genes
GSVA gene sets RNA-seq
updated 2.3 years ago by ★ 3.0k • written 2.3 years ago by ▴ 60
0
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3
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573
views
Weird set of samples in plant gene atlas study that appear over-corrected after DESeq2 normalization
RNA-Seq DESeq2
updated 2.3 years ago by 39k • written 2.3 years ago by • 0
0
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0
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850
views
how to find consensus modules between 2 datasets by different platform through WGCNA
consensusmodule microarray RNA-seq WGCNA
2.3 years ago modarzi ▴ 10
0
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0
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518
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Job: Bioinformatics Developer / Computational Biologist
bioinformatics rna-seq shiny apps R algorithm development Job
2.3 years ago mmartin ▴ 20
0
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0
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466
views
circRNAprofiler - miRNA binding sites
circRNA RNA-seq circRNAprofiler
2.3 years ago Terra • 0
0
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0
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746
views
HISAT2/StringTie/Ballgown for Novel Transcript Isoform Differential Expression
isoform RNA-seq hisat2 stringtie ballgown
2.3 years ago ra711 • 0
3
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3
replies
666
views
Problem to understand Interactions at any time
RNA-seq edgeR interactions
updated 2.4 years ago by 47k • written 2.4 years ago by ▴ 10
0
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3
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687
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Pathway analysis of bacterial RNA-seq data
annotation rna-seq pathway analysis
2.4 years ago microPhD • 0
5
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6
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934
views
RUVseq to remove a library size artefact in a zebrafish brain RNA-seq dataset
RUVSeq RUV RNA-seq
updated 2.4 years ago by 62k • written 2.4 years ago by ▴ 20
3
votes
1
reply
497
views
How do you create a targets dataframe in edgeR?
edgeR RNA-SEQ
updated 2.4 years ago by 62k • written 2.4 years ago by • 0
1
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1
reply
641
views
Having issues mapping gene Ids during ReportingTools::publish() from Bioconductor.
ReportingTools RNA-Seq RMarkdown
updated 2.4 years ago by 62k • written 2.4 years ago by ▴ 20
1
vote
4
replies
883
views
Issues with DESeq2 LRT for time-course experiment
rna-seq R DESeq2 LRT
updated 2.5 years ago by 3.7k • written 2.5 years ago by ▴ 10
0
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1
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497
views
dupRadar: low % of duplicates for 150bp PE RNAseq
dupRadar 150bp RNA-seq
updated 2.5 years ago by ▴ 80 • written 2.5 years ago by • 0
0
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4
replies
925
views
Using different LFC shrinkage estimators for spike-in normalised RNA-seq data
deseq2 apeglm rna-seq spike-in
updated 2.5 years ago by 39k • written 2.5 years ago by • 0
2
votes
2
replies
2.6k
views
Calculation of module membership in WGCNA
WGCNA RNA-seq ModuleMembership Network Hub gene
updated 8 months ago by ▴ 10 • written 2.5 years ago by ▴ 50
0
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0
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538
views
Job: Scientist 1, Bioinformatics (Research | Berkeley, CA | Full Time)
Bioinformatics drug-discovery RNA-seq CRISPR Job
2.5 years ago yzhang • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: DESeq2 and heatmap for multiple comparisons by artem.vorobyev • 0
this I already did. My question is how to visualize differentially expressed genes on the heatmap for all 3 groups (healty->lesion->treat…
Comment: athPkgBuilder data source :missing probesets by nicklesteele532 • 0
> >>> > >>> How to handle the one probeset to multiple locus mappings? I can > >think 3 > >>> possible solutions: > >>> 1. pick the "best" …
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
> sum(width(gr_toexclude)) [1] 2713499861 I excluded everything which was not locus. If small rna locus is from 2000 to 4000 and next locu…
Comment: Why in Bioconductor community people rarely upvote questions? by Hervé Pagès 16k
BTW I fail to see how the lack of upvotes to a question would be discouraging as long as you get a good answer. OTOH I can see how failing …
Answer: DESeq2 and heatmap for multiple comparisons by swbarnes2 ★ 1.2k
If you want to know what genes are different between lesion and treated, compare them to each other.
Votes
Comment: recount 3 protect read length metadata
Answer: Doubts about manipulation and annotation of microarray files deposited at GEO
C: Batch correction in DESeq2
Comment: Strand information in a GAlignmentsList object derived from strand-specific pair
Comment: Strand information in a GAlignmentsList object derived from strand-specific pair
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