Showing : differential expression • reset
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Moderated F-test followed by moderated t-test in limma
limma differential expression
updated 3.7 years ago by 50k • written 3.7 years ago by • 0
5
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3
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1.3k
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Latent factors for differential expression
deseq2 zinbwave 10X scRNA-seq Differential expression
updated 3.8 years ago by 41k • written 3.8 years ago by ▴ 20
3
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1
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1.0k
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Obtain p-values for group * condition interaction using DESeq2?
DESeq2 interaction differential expression
updated 3.8 years ago by 41k • written 3.8 years ago by ▴ 160
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5
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2.3k
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edgeR + tximport: calcNormFactors and the usage of offsets
edgeR tximport differential expression
4.0 years ago hollandademello ▴ 20
1
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1
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1.6k
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Differential expression on Nanostring normalised protein data
R Differential expression
updated 4.0 years ago by ★ 3.9k • written 4.0 years ago by • 0
2
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2
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690
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edgeR - Correct approach to compare abundances of genomic regions?
edger differential expression
updated 4.1 years ago by 50k • written 4.1 years ago by ▴ 20
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0
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693
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Problems with cummeRbund
plot transcriptomics differential expression cummeRbund
4.1 years ago raquelponti • 0
0
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1
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673
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using deseq2 for intronic counts for 2 conditins with replicates
deseq2 intron differential expression
updated 4.1 years ago by 41k • written 4.1 years ago by ▴ 40
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4
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1.3k
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Agilent two-color microarray analysis with limma: 2x3 factorial design
limma microarray contrast matrix 2x3 factorial design differential expression
updated 4.0 years ago by 50k • written 4.1 years ago by • 0
4
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7
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1.1k
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'NA' found under Gene Names in the list of top differentially expressed genes found using edgeR
edger differential expression TCGA Gene ID
updated 4.1 years ago by 65k • written 4.1 years ago by ▴ 60
7
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4
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4.2k
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Limma when to use zero intercept
limma regression differential expression linear model
updated 4.2 years ago by 50k • written 4.2 years ago by • 0
2
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3
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1.4k
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DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2 deseq differential expression contrasts
updated 4.5 years ago by 41k • written 4.5 years ago by ▴ 180
2
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1
reply
634
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Detecting the power in differential expression
POWER DESEQ2 edger LIMMA DIfferential expression
4.5 years ago • updated 4.4 years ago Beginner • 0
0
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1
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784
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How to handle batch effect and interaction with experimental variables
deseq2 statistics differential expression
4.5 years ago A • 0
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0
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1.4k
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GDCprepare error in TCGAbiolinks
tcgabiolinks gdcprepare differential expression
4.5 years ago fawazfebin ▴ 60
8
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11
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2.4k
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dream vignette says limma-voom repeated measures two-group comparison needs two duplicateCorrelation rounds which differs from limma user's guide and…
dream variancePartition limma differential expression repeated measures
updated 4.6 years ago by 50k • written 4.6 years ago by ▴ 20
5
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8
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1.8k
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Unexpected results while analyzing a subset of genes in GEO RNAseq dataset containing TPM values
R limma TPM rnaseq differential expression
updated 4.6 years ago by ★ 13k • written 4.6 years ago by ▴ 30
3
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2
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1.8k
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Variation between technical replicates (DESeq2, batch effects)
rnaseq deseq2 differential expression batch effect replicates
updated 4.6 years ago by 41k • written 4.6 years ago by ▴ 10
5
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6
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1.3k
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is our edgeR code doing what we think it does?
edger differential expression rna-seq
updated 4.7 years ago by ▴ 840 • written 4.7 years ago by ▴ 10
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1
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1.6k
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Minimum number of cells required for the MAST
MAST scRNAseq differential expression
4.7 years ago Andrew_McDavid ▴ 270
2
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4
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1.3k
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Majority upregulated genes in edgeR
edger differential expression genes fold change
updated 4.9 years ago by ★ 28k • written 4.9 years ago by • 0
1
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1
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998
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All Pairwise Comparisons with DESeq2 While Controlling for Batch Effects: Does Reference Level Matter?
deseq2 differential expression batch correction design
updated 4.9 years ago by 41k • written 4.9 years ago by ▴ 40
4
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4
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1.3k
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Batch Correction: DESeq2 Linear Model vs Batch-Correction-Specific Algorithms (RUV, ComBat, ect.)
deseq2 differential expression batch correction
updated 4.9 years ago by 41k • written 4.9 years ago by ▴ 40
1
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12
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1.4k
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RNA-Seq and edgeR: remarkable differences between cpms and fitted values
RNA-Seq edger fitted values differential expression normalization
updated 4.9 years ago by 50k • written 4.9 years ago by ▴ 90
4
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5
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3.2k
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How does limma calculate the log2fc?
Limma Differential Expression Time-course Analysis
updated 5.0 years ago by 50k • written 5.0 years ago by ▴ 10
1
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1
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880
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How to normalize RNA-seq when 50% genes are DE? (TMM)
limma TMM differential expression normalization rnaseq
updated 5.1 years ago by 65k • written 5.1 years ago by • 0
0
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1
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1.1k
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Scran: Performing DE after cell-typle identifaction on the corrected and integrated datasets
Scran MNN_correct Differential expression single-cell
5.1 years ago baldissera152 • 0
5
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1
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1.2k
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Limma - Using removeBatchEffect before differential expression analysis
limma batch effect differential expression
updated 5.2 years ago by 65k • written 5.2 years ago by • 0
3
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3
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3.3k
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Using PEER to identify hidden confounders in RNA-seq data (not working)
PEER RNA-seq differential expression hidden confounders
updated 2.1 years ago by ▴ 30 • written 5.3 years ago by ▴ 30
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3
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1.5k
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How to handle replicates and treatment conditions in TissueEnrich package
rna-seq TissueEnrich tissue-specific expression differential expression
updated 5.3 years ago by ▴ 10 • written 5.3 years ago by • 0
1
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1
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1.3k
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PLAGE method fails in GSVA if an overlap between gene sets and genes in expressions is less than two
gsva plage differential expression gene set enrichment
5.3 years ago krassowski.michal ▴ 40
2
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7
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2.1k
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Get the countsFromAbundance as limma input
tximport limma deseq2 differential expression
updated 5.7 years ago by 50k • written 5.7 years ago by • 0
15
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12
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2.5k
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ZINB-WaVE + DESeq2 misses low-expressed, single-condition genes that look like they should be markers
deseq2 ZINB-WaVE single cell RNA-seq differential expression
updated 5.7 years ago by 41k • written 5.7 years ago by ▴ 60
1
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3
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1.5k
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Global expression shift using RUVSeq
ruvseq rnaseq normalization differential expression
updated 5.8 years ago by ▴ 950 • written 5.8 years ago by • 0
1
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4
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1.5k
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venDiagram after limma showing more genes after specifying up or down regulated specifically
venn diagram venndiagram limma microarray differential expression
updated 5.8 years ago by 65k • written 5.8 years ago by ▴ 40
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1.0k
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DE analysis when large portion of transcriptome is changed
rna-seq edger ebseq differential expression
updated 5.8 years ago by ★ 28k • written 5.8 years ago by • 0
1
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4
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DE analysis of orthologs with varying sequence lengths using RSEM+tximport+DEseq2: normalization for sequence length?
deseq2 sequence length normalization RSEM tximport differential expression
updated 5.9 years ago by 41k • written 5.9 years ago by ▴ 50
22
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17
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7.2k
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DESeq2 1.20.0 lfcshrink function
deseq2 differential expression logfoldchange lfcshrink lfcthreshold
updated 2.9 years ago by 41k • written 5.9 years ago by ▴ 30
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4
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1.4k
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Deseq2 problem visualizing gene expression with batch corrected values
deseq2 limma differential expression visualization
updated 5.9 years ago by 41k • written 5.9 years ago by • 0
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0
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989
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pair wise ballgown
ballgown differential expression
5.9 years ago zoe.ward • 0
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0
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1.2k
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Ballgown normalisation... why are still using FPKM?
rnaseq normalization differential gene expression differential expression
5.9 years ago manuelmendoza • 0
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6
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1.3k
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differential expression analysis with big dataset and >500 surrogate variables
SVA deseq2 differential expression LRT
6.0 years ago aec ▴ 90
0
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1
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959
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Interpretation of p-value plot
p values differential expression limma
updated 6.0 years ago by 50k • written 6.0 years ago by • 0
5
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4
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1.2k
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Finding genes respond differently to treatment between many genotype comparison
edgeR nested design differential expression
updated 6.0 years ago by 50k • written 6.0 years ago by • 0
0
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3
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892
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interaction model deseq2 specific DE genes
deseq2 interaction model differential expression
updated 6.0 years ago by 41k • written 6.0 years ago by ▴ 90
6
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4
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1.4k
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Fitting Gamma GLMs for examining differential expression
deseq2 edger differential expression
updated 6.1 years ago by ★ 7.9k • written 6.1 years ago by ▴ 10
7
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11
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2.6k
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Analysis of pathways using edgeR
rnaseq differential expression edgeR kegg
updated 6.2 years ago by 50k • written 6.2 years ago by ▴ 60
2
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1
reply
4.7k
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Using DESeq2 to analyse TCGA data
deseq2 tcga tcgabiolinks gene expression differential expression
updated 6.2 years ago by 41k • written 6.2 years ago by • 0
1
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4
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2.2k
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How to perform time-course differential expression with "erroneous" baseline in edgeR?
edger differential expression timecourse
updated 6.2 years ago by 50k • written 6.2 years ago by • 0
1
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3
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1.4k
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Differential expressiong with two groups in BASiCS
BASiCS single-cell bayesian differential expression
updated 6.2 years ago by ▴ 10 • written 6.2 years ago by ▴ 10
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Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
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Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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