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Showing top results for tag: normalization • reset
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149
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Best Practices for Handling Negative Values in MFI Data after log base 2 transformation with median normalization
normalization statistics log-transformation
updated 2 days ago by 44k • written 2 days ago by • 0
0
votes
0
replies
103
views
How to normalize gene abundance from long read metagenomic data?
normalization metagenomics long-read gene-abundance
3 days ago by Adrián • 0
1
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0
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219
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What is the right choice of normalization and preprocessing before WGCNA using RNAseq data in a cohort?
normalization RNA_seq cohort WGCNA
18 days ago by sukeshinik5 ▴ 50
1
vote
2
replies
361
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Questions Regarding Normalization and Standardization in RNA-seq Differential Analysis
RNA-seq Normalization
updated 20 days ago by 44k • written 21 days ago by ▴ 10
7
votes
24
replies
1.5k
views
TCGA Biolinks code issue
normalization TCGAbiolinks
updated 28 days ago by ▴ 100 • written 4 weeks ago by ▴ 30
2
votes
1
reply
734
views
Understanding behaviour of SCTransform in Seurat
Seurat scRNASeq normalization
updated 5 weeks ago by • 0 • written 5 months ago by ▴ 600
1
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3
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449
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NA Values Appearing After Log Transformation of array Data
normalization
updated 8 weeks ago by ★ 4.4k • written 8 weeks ago by • 0
0
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0
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168
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Functional normalization using minfi::preprocessFunnorm and control PCs in later analyses
normalization EWAS epigenome preprocessing
updated 9 weeks ago by 44k • written 9 weeks ago by • 0
3
votes
6
replies
626
views
normalization in single cell
normalization scRNA-seq single-cell
updated 10 weeks ago by 5.8k • written 10 weeks ago by ▴ 20
0
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0
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198
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Using get_normalized_expression (scVI) vs. Log-Normalized Counts
scVI normalization RNA-seq single-cell UMAP
10 weeks ago by Nicolas • 0
0
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2
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295
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normalizing multiple conditions together or not
normalization edgeR
3 months ago by markus.glass ▴ 40
0
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0
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212
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SMART-seq normalizarion and integration
SMART-seq single-nuclei normalization RNA-seq single-cell
3 months ago by vigbr ▴ 20
2
votes
3
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6.0k
views
DESeq2 vst function error
DESeq2 RNA-Seq R normalization
updated 3 months ago by ★ 4.3k • written 4.2 years ago by ▴ 90
7
votes
5
replies
1.8k
views
7 follow
How to normalize long-read RNA-seq data for comparison with short-reads
RNAseq long-reads normalization short-reads
updated 3 months ago by 146k • written 21 months ago by ▴ 30
0
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0
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196
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Calculation of RPM and deduplication
normalization metagenomics RPM deduplication
3 months ago by Luca Arbore • 0
2
votes
5
replies
387
views
Normalizacion RNASeq Doubts
normalization bacteria featureCounts RNA-seq
updated 3 months ago by 44k • written 3 months ago by • 0
1
vote
1
reply
258
views
DESeq2 sizeFactor for Bacterial RNASeq
normalization bacteria rRNA RNASeq
updated 3 months ago by 14k • written 3 months ago by • 0
0
votes
2
replies
649
views
Should I normalize and scale my data again after doing subset(seu, idents=" ") in Seurat?
normalization seurat scRNA-seq
4 months ago by ev97 ▴ 40
8
votes
4
replies
532
views
Normalization of samples with very different transcriptomic profiles
DESeq2 normalization RNA-seq edgeR DGE
updated 4 months ago by 85k • written 4 months ago by • 0
0
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0
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170
views
Creation of appropriate model matricies for Surrogate Variable Analysis (SVA)
normalization rna-seq sva microarray
4 months ago by qile0317 • 0
0
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0
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248
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Subset of ATAC-seq peaks has high variance
atac-seq edgeR R normalization
5 months ago by Tim • 0
1
vote
3
replies
588
views
How to compute TPM normalized values for TCGA miRNA data?
TCGA normalization TPM miRNA
updated 5 months ago by 14k • written 5 months ago by • 0
0
votes
5
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1.4k
views
6 follow
What purposes can TPM values be used for?
RNA-seq TPM Normalization DESeq2
updated 6 months ago by ▴ 300 • written 6 months ago by • 0
5
votes
2
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530
views
ChIP-seq datasets: input samples omitted?
ChIP-seq Normalization NGS
updated 6 months ago by 20k • written 6 months ago by ▴ 40
1
vote
1
reply
409
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing housekeeping Single-cell normalization
updated 6 months ago by 85k • written 6 months ago by • 0
2
votes
4
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587
views
from row count to tpm
tpm row-count normalization
updated 6 months ago by 44k • written 6 months ago by ▴ 20
1
vote
5
replies
1.0k
views
RNA seq differential expression analysis
RNA-seq normalization
updated 6 months ago by ★ 2.1k • written 6 months ago by • 0
3
votes
1
reply
749
views
What is the normalization status of metabric data?
metabric normalization microarray cbioportal
updated 6 months ago by ▴ 20 • written 2.1 years ago by ★ 4.3k
0
votes
2
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452
views
Abundance Calculation in MetaPhlAn 3: Methodology, TPM or RPKM, and the Treatment of Unclassified Reads
MetaPhlAn Normalization RPKM TPM
6 months ago by ramin.k2013 • 0
0
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0
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248
views
Normalization in Metagenomics Sequencing By Total Number of Reads: Pre- or Post-Filtering and the Role of Unclassified Reads
Normalization Metagenomics
updated 6 months ago by 44k • written 6 months ago by • 0
0
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0
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231
views
Methylation array analysis using dmpFinder
epic methylation normalization dmp mset
6 months ago by Roy ▴ 10
0
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0
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209
views
How can I plot the PCA with the raw count mRNA seq data?
PCA normalization
updated 6 months ago by 44k • written 6 months ago by ▴ 20
0
votes
1
reply
321
views
Normalization strategies for comparing mapped reads across samples in RNA-seq
normalization rnaseq
updated 7 months ago by 44k • written 7 months ago by ▴ 650
1
vote
3
replies
709
views
DESeq2 and normalization
RNA-seq normalization DESeq2
updated 7 months ago by ★ 6.9k • written 7 months ago by • 0
0
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0
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269
views
scRNA Cell Clustering Defined by Normalized Counts
Normalization scRNA Seurat
7 months ago by sakura • 0
2
votes
2
replies
460
views
How to visualize scRNA-seq normalized data
Seurat 10x scRNA-Seq Single-cell normalization
7 months ago by SlowSD • 0
1
vote
3
replies
523
views
RNA-seq bam file normalization
RNA-seq bam normalization
updated 8 months ago by ★ 6.9k • written 8 months ago by ▴ 20
12
votes
7
replies
5.8k
views
6 follow
Convert FPKM to TPM in R
r TPM normalization meta-analysis
updated 8 months ago by 44k • written 2.1 years ago by ▴ 160
1
vote
4
replies
635
views
perplexed regarding the process of gene expression normalision
gene RNA-seq expression normalization
8 months ago by DS ▴ 10
0
votes
3
replies
616
views
Normalization of combined normal and tumor tissue samples from GTEx and TCGA prior to CIBERSORTx devconvolution
gtex cibersort tcga rna normalization
updated 8 months ago by ★ 1.8k • written 8 months ago by ▴ 10
1
vote
3
replies
555
views
GTEx TPMs Vs normalized data
gtex RNA-seq normalization gene-expression
updated 8 months ago by ★ 1.8k • written 8 months ago by ▴ 10
11
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4
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1.1k
views
Why employ normalization methods, and how can they be utilized in DEG analysis?
R DEGs normalization
7 months ago by wyt1995 ▴ 40
0
votes
3
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608
views
csaw - is there a way to identify composition bias in a dataset?
chip-seq csaw normalization composition-bias
updated 9 months ago by 85k • written 9 months ago by ▴ 10
0
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0
replies
252
views
Comparing relative expression of a conserved gene between distantly related species.
RNAseq ComparativeGenomics Normalization
9 months ago by georgii.vdovin • 0
0
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0
replies
260
views
Normalization of allelic counts for allele-specific expression analysis
allelic-ratio allelic-counts normalization allele-specific-expression RNA-seq
updated 9 months ago by 44k • written 9 months ago by ▴ 10
0
votes
3
replies
580
views
WGCNA Soft Power Problem
normalization wgcna RNA-seq DESeq2
updated 9 months ago by 4.3k • written 9 months ago by • 0
0
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0
replies
312
views
How to normalize for Correlation network with two different parameters
Correlation Normalization
10 months ago by Mary • 0
5
votes
5
replies
869
views
Normalization and Genome-Wide Comparisons with Chipseq
chip-seq Chipseq Normalization
updated 10 months ago by ▴ 500 • written 10 months ago by ▴ 10
1
vote
2
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635
views
Comparing 3 Data Sets using DeSeq and Heatmaps
DESeq2 Normalization
updated 10 months ago by 44k • written 11 months ago by • 0
0
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0
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298
views
Best Preprocessing Approach for Tissue Microarray Data: Separate or Post-Merger Normalization?
normalization array
11 months ago by rk.khayami94 ▴ 10
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What about some of the well known enhancer regions, the globin locus LCR? Likely to be highly sequenceable, and yet not on exome panels.
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