Showing : rnaseqdata • reset
1
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DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 23 months ago by 53k • written 2.1 years ago by • 0
0
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1
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1.1k
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Comparing RNASeq data from multiple studies
RNASeqData RnaSeqSampleSize RNASeqPower RNASeq
updated 2.1 years ago by ▴ 780 • written 2.1 years ago by • 0
2
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4
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1.6k
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Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData DifferentialExpression SmallRNAData DESeq2
2.1 years ago Shihui • 0
0
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4
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1.4k
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filtering out lowly expressed genes by groups
RNASeqData DESeq2
updated 2.1 years ago by 68k • written 2.1 years ago by ▴ 10
3
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3
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3.4k
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Differential expression analysis with only FPKM matrix available from total newbie in R
FPKM RNASeqData DEAnalysis limma
2.1 years ago Ethan Nguyen • 0
1
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1
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1.6k
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Can I transform already normalized rna-seq data with Z-score?
Z-score RNASeqData Deseq DESeq2
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
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2
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1.0k
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RSubread DESeq2
RNASeqData DifferentialExpression DESeq2
2.1 years ago Beyza • 0
1
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1
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905
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bulk RNA-Seq batch correction
RNASeqData rnaseqcomp RNASeq
updated 2.1 years ago by ★ 5.0k • written 2.2 years ago by • 0
0
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0
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639
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How to use erccdashboard with erccmix="Single" design
RNASeqData erccdashboard
2.2 years ago • updated 2.1 years ago adi.rotem • 0
0
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1
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831
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Is it possible to combine count gene expression data coming from one sequencing technology (RNA seq) with intensity gene expression data coming from …
DESeq2 RNASeqData edgeR limma DifferentialExpression
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by • 0
0
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1
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990
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Why was the number of DEG different between DESeq results and count by myself using excel?
RNASeqData DEGseq
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by • 0
2
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3
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3.0k
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bulk RNA-seq analysis using R : batch effect : One question concerning Combat-seq and one question concerning DESeq2 design = batch + condition
BatchEffect sva DESeq2 RNASeqData limma
updated 2.2 years ago by 68k • written 2.2 years ago by ▴ 10
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2
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2.4k
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understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData Rsubread mapping featurecounts
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
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2
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3.1k
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DESeq2 discrepancy in log2FC significance and normalized counts significance
RNASeqData DESeq2
2.2 years ago Marina • 0
1
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2
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2.7k
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IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon IsoformSwitchAnalyzeR tximport RNASeqData
updated 2.3 years ago by ▴ 120 • written 2.3 years ago by ▴ 10
0
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6
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1.4k
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Questionable limma results for differential expression on RNA-seq
RNASeqData DifferentialExpression limma
updated 2.3 years ago by 53k • written 2.3 years ago by • 0
1
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2
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878
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I changed the reference in DGE contrasts by DESeq2, but the results changed just a bit and not in the sign of Log2FC (positive to negative and invers…
RNASeqData DESeq2
updated 2.3 years ago by 43k • written 2.3 years ago by • 0
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0
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806
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BubbleGUM for multi group comparison of gene set enrichment
RNASeqData GeneSetEnrichment multiGSEA
2.3 years ago sonal • 0
1
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9
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1.5k
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DESeq2 not replicable results
RNASeqData DESeq2
updated 2.3 years ago by 43k • written 2.3 years ago by • 0
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0
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1.0k
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News: Course - Network Analysis in Systems Biology with R/Bioconductor
Bioconductor Network RNASeqData SystemsBiology
2.3 years ago info ▴ 10
2
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1
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1.3k
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DESeq2 time course using fitted splines
RNASeqData TimeCourse DESeq2 timecoursedata
updated 16 months ago by 43k • written 2.3 years ago by • 0
1
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1
reply
797
views
Best way to handle batch effects from difference Mice?
RNASeqData BatchEffect edgeR limma
updated 2.3 years ago by 53k • written 2.3 years ago by • 0
2
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1
reply
1.8k
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Using oligo or xps to read and convert RNA-seq data CEL file to txt file.
oligoData DataImport oligo RNASeqData convert
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
0
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1
reply
947
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Controlling for covariates and identifying DEGs using DESeq2
RNASeqData DESeq2
updated 2.3 years ago by 43k • written 2.3 years ago by ▴ 20
3
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3
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2.5k
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how to remove batch effects of RNA seq data based on continuous variables(like surrogate variables from sva package) using combatseq or limma (remove…
combatseq RNASeqData sva limma
2.3 years ago amnahsiddiqa ▴ 10
2
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3
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2.5k
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC RNASeqData sva BatchEffect
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by ▴ 10
0
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0
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855
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How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData BatchEffect sva
2.3 years ago amnahsiddiqa ▴ 10
1
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1
reply
990
views
DESEQ2 differential expression for subsets of data?
RNASeqData DESeq2
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by ▴ 10
0
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1
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869
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How to do PFS after Voom + Limma DGE ?
RNASeqData limma voom PFS DGE
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
3
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2
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1.2k
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Does this RNAseq experiment require a repeated measures approach?
StatisticalMethod RNASeqData edgeR DESeq2
updated 2.4 years ago by 53k • written 2.4 years ago by ▴ 30
0
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2
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1.0k
views
RNA seq differential expression analysis
DEGseq RNASeqData limma
updated 2.4 years ago by 53k • written 2.4 years ago by • 0
0
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1
reply
828
views
Design formula for genotype-specific condition effects using ~group in the design
RNASeqData DifferentialExpression DESeq2
updated 2.4 years ago by 43k • written 2.4 years ago by • 0
2
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5
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2.3k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 18 months ago by • 0 • written 2.4 years ago by • 0
1
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1
reply
706
views
Deseq contrast question
RNASeqData DESeq2
updated 2.4 years ago by 43k • written 2.4 years ago by ▴ 10
0
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1
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949
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DESeq2 about comparasion of gene expression change on two-time points between two group samples.
DESeq2 RNASeqData edgeR limma DifferentialExpression
updated 2.4 years ago by ★ 1.4k • written 2.4 years ago by • 0
0
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4
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2.1k
views
enhanced volcano , different -log10pvalue of the same gene
EnhancedVolcano RNASeqData DifferentialExpression
2.5 years ago ruba-mahmoud • 0
2
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3
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3.2k
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RNA-seq analysis without replicates
DESeq2 RESEQ RNASeqData
updated 2.6 years ago by • 0 • written 2.6 years ago by • 0
0
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2
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1.2k
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Is there any reason to think that normalization (e.g. TMM) doesn't work well with samples that that have very different raw counts?
limma RNASeqData edgeR
updated 2.7 years ago by ▴ 40 • written 2.7 years ago by • 0
2
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5
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2.7k
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edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR RNASeq RNASeqData Bioconductor
written 2.7 years ago by • 0
0
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2
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1.2k
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RNA-Seq and disease outcome analysis
rnaseqAnalysis RNASeqData
2.7 years ago JonasEnder • 0
0
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3
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1.4k
views
Understanding edgeR differential expression results
Transcriptomics edgeR DifferentialExpression RNASeqData RNASeq
updated 2.7 years ago by 53k • written 2.7 years ago by • 0
1
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2
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1.3k
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Installation of R-packages for RNA-seq analysis
RNASeqData
2.7 years ago Begin-R • 0
0
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1
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866
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How to find degraded genes but unaffected by condition in a time course RNAseq experiment ?
DESeq2 RNASeqData DifferentialExpression
updated 2.8 years ago by ★ 5.0k • written 2.8 years ago by • 0
0
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1
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753
views
Differential RNA seq on TCGA set
DESeq2 RNASeqData
updated 2.8 years ago by ★ 5.0k • written 2.8 years ago by • 0
1
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4
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2.5k
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Inverted Log2FC values after DEseq2 analysis
DESeq2 Log2FC RNASeqData
2.8 years ago Iwan • 0
0
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1
reply
892
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Using DESeq2 for time-series analysis with two conditions
DESeq2 RNASeqData
updated 2.9 years ago by ★ 5.0k • written 2.9 years ago by • 0
0
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3
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2.3k
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 15 months ago by • 0 • written 3.0 years ago by • 0
0
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0
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726
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how to create PHENO_DATA
RNASeq RNASeqData RNASeqRData
3.1 years ago marymshahi2021 • 0
3
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2
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5.3k
views
Understanding how to contrast two treatments in DESeq2
DESeq2 RNASeqData
updated 3.2 years ago by ★ 1.4k • written 3.2 years ago by • 0
0
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0
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600
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Can I loosely say that a gene is expressed by simply look at the gene count from RNA-Seq?
RNASeqData RNASeq
3.2 years ago Pang • 0
151 results • Page 2 of 4
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Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
I can reproduce this and have opened an issue on the code base https://github.com/Bioconductor/support.bioconductor.org/issues/112
Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
we can investigate this issue. thank you for bringing it to our attention
Comment: deseq2 filter the low counts by Michael Love 43k
> But within each comparison (contrast), if I trace some DEGs back to the original salmon merged gene counts (or even to normalised counts)…
Comment: deseq2 filter the low counts by empty_mt • 0
Thank you for you suggestion to look at the pre-filtering section in the DESeq2 vignettes - am I missing something? I have 6 treatments, …
Comment: deseq2 filter the low counts by Michael Love 43k
Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering
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Bioconductor 3.22 Released!
Comment: "Watched Tags" are being erased rather than updated
Comment: deseq2 filter the low counts
Answer: DESeq2 interactions
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