Limit : all time
all time today this week this month this year
50 results • Page 1 of 1
Sort: Rank
Rank Views Votes Replies
Showing top results for tag: PCA • reset
9
votes
5
replies
26k
views
PC3 & PC2 using plotPCA function in R
R plotPCA PCA
updated 1 day ago by 44k • written 7.6 years ago by ▴ 710
1
vote
2
replies
166
views
Dealing with outliers for differential expression in proteomics
proteomics PCA DEA outliers limma
updated 1 day ago by 85k • written 1 day ago by • 0
0
votes
0
replies
130
views
News: Multivariate Data Analysis with R and vegan course
Multivariate Ordination-Methods PCA PCoA
4 days ago by carlopecoraro2 ★ 2.6k
2
votes
4
replies
307
views
coordinate vs contributions for the variables in PCA using FactoMineR
PCA
updated 8 days ago by 5.8k • written 8 days ago by ▴ 60
1
vote
4
replies
327
views
Bulk RNA seq PCA plot issues
RNA-seq PCA
updated 10 days ago by 44k • written 10 days ago by • 0
2
votes
0
replies
144
views
Blog: How Seurat PCA projection, KNN and MNN for label transfer work
R RNA-seq scRNA-seq PCA
updated 10 days ago by 44k • written 11 days ago by ★ 4.4k
106
votes
109
replies
52k
views
29 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 12 days ago by 4.3k • written 6.2 years ago by 88k
3
votes
6
replies
439
views
PCA for count data
PCA
16 days ago by QX ▴ 60
0
votes
0
replies
182
views
Help with EIGENSOFT's SmartPCA
SmartPCA EIGENSOFT PCA
24 days ago by Junaid • 0
0
votes
5
replies
566
views
Issue understanding ATAC-seq PCA
ATAC-seq PCA
updated 4 weeks ago by 4.3k • written 4 weeks ago by ▴ 10
4
votes
5
replies
620
views
LD Pruning in GWAS
PLINK PCA pruning LD GWAS
updated 9 weeks ago by 4.5k • written 9 weeks ago by ▴ 30
0
votes
2
replies
503
views
Explaining my heatmap for PC1 and my PC2 with gene list
pca heatmap
updated 9 weeks ago by 88k • written 3 months ago by • 0
0
votes
1
reply
273
views
PCA Genotyping rate 1000genome and own data
quality genotypingrate pca plink genomics
updated 3 months ago by 4.3k • written 3 months ago by • 0
1
vote
0
replies
165
views
Removal of samples with weird log-CPM distribution or voomWithQualityWeights?
voomWithQualityWeights limma PCA outliers
3 months ago by t.fortunato.asquini ▴ 10
0
votes
1
reply
281
views
PCA Visualization error in R - arguments imply differing number of rows
SNPs PCA GBS LINUX r
updated 5 months ago by 12k • written 5 months ago by • 0
4
votes
9
replies
1.0k
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA R VARIANCE
updated 5 months ago by ▴ 150 • written 5 months ago by ▴ 20
0
votes
2
replies
394
views
Error in plotting PCA plot in seurat
PCA single-cell seurat scRNA RNA
updated 5 months ago by 44k • written 5 months ago by • 0
0
votes
1
reply
359
views
Finding batch and outlayers
Pca
updated 6 months ago by ▴ 460 • written 6 months ago by • 0
0
votes
0
replies
284
views
scRNA Cluster frequency
CV PCA scRNA Cluster-Frequency
6 months ago by Nitin • 0
0
votes
2
replies
471
views
WGCNA
PCA WGCNA EIGENGENE
6 months ago by rajasekargutha ▴ 60
0
votes
0
replies
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
1
vote
2
replies
676
views
Putting colors of different samples on PCA plot
PCA
updated 6 months ago by 44k • written 6 months ago by • 0
0
votes
0
replies
276
views
details about PCA in plink 2.0: eigenvectors, PCs, scores
gwas plink pca
7 months ago by kaybelter • 0
0
votes
1
reply
376
views
PCA script correction
correction script PCA
updated 7 months ago by ★ 2.1k • written 7 months ago by • 0
1
vote
6
replies
719
views
Quest about the input data for PCA analysis
PCA
7 months ago by tujuchuanli ▴ 130
2
votes
3
replies
557
views
representing PCs as marginal distribution on x and Y acis
PCAtool Deseq2 Pcaplot PCA
updated 7 months ago by ★ 3.0k • written 7 months ago by • 0
0
votes
4
replies
543
views
PCA Plot in Single-cell RNA-seq Data
RNA-seq PCA single cell
8 months ago by Darya • 0
1
vote
2
replies
648
views
PCA results from PLINK and Hail vastly different
gwas plink hail pca
updated 8 months ago by 11k • written 8 months ago by • 0
0
votes
6
replies
925
views
Making PCA plot using variance instead of counts on Sleuth (plot_pca)
Sleuth RNAseq PCA
updated 8 months ago by 44k • written 8 months ago by • 0
4
votes
1
reply
442
views
What does PCA really tells about Biological data?
techniques reduction Dimension PCA
updated 8 months ago by 8.7k • written 8 months ago by ▴ 810
0
votes
5
replies
743
views
PCA from plink2 for SGDP using a pangenome and DeepVariant
umap DeepVariant pangenome plink2 pca
updated 8 months ago by ▴ 450 • written 8 months ago by ▴ 100
7
votes
8
replies
969
views
8 follow
PCA plot interpretation (single population)
PCA GWAS pruning
updated 5 weeks ago by • 0 • written 9 months ago by ▴ 20
1
vote
2
replies
694
views
Should centering and scaling be done on methylation beta values for principal component analysis (PCA)?
PCA PCAtools
9 months ago by Pratik ★ 1.1k
0
votes
5
replies
722
views
An question about PCA analysis of protein data in R
PCA
updated 10 months ago by 44k • written 10 months ago by • 0
1
vote
10
replies
3.0k
views
Scanpy Pearson residual PCA error
python scRNA scanpy PCA
updated 11 months ago by • 0 • written 2.2 years ago by ▴ 70
2
votes
3
replies
627
views
Dimensionality reduction on data sets with variable dimensions
PCA dimensionality_reduction RNA_secondary_structure
updated 10 months ago by ★ 28k • written 11 months ago by ▴ 80
1
vote
9
replies
3.7k
views
PCAtools data file not linking to metadata file
R PCA RNA-Seq PCAtools
updated 11 months ago by 85k • written 4.4 years ago by ▴ 10
4
votes
6
replies
880
views
Unexpected separation of RNA-seq samples on PCA plot
depletion PCA rRNA plot RNA-seq
11 months ago by Tihana ▴ 10
0
votes
0
replies
455
views
Seurat: Visualize individual cell clusters colored by meta.data variable
UMAP PCA Seurat
12 months ago by Sergio • 0
7
votes
13
replies
1.3k
views
deal with PCA and my samples
PCA DEG meta-analysis
12 months ago by ali • 0
1
vote
2
replies
613
views
Which embedding for clustering of cells in single-cell RNAseq?
tSNE ICA clustering PCA UMAP
12 months ago by e.r.zakiev ▴ 230
0
votes
2
replies
2.3k
views
Removing constant/zero columns for PCA?
R pca
updated 12 months ago by ★ 28k • written 12 months ago by ▴ 150
2
votes
5
replies
1.3k
views
Number of accessible regions included by DESeq2 to generate the PCA plot with the nf-core ATACseq pipeline ?
nf-core atac-seq PCA DESeq2
updated 13 months ago by ★ 2.6k • written 13 months ago by • 0
0
votes
0
replies
320
views
Question about umap using different numbers of pca components as initialization
umap pca dynamo scRNAseq
14 months ago by Zack • 0
8
votes
9
replies
1.7k
views
PCA proteomic DEP
PCA DEP
updated 14 months ago by 88k • written 14 months ago by ▴ 370
0
votes
0
replies
573
views
Principal component analysis (PCA) from Desmond output file
Desmond PCA prody Simulation
14 months ago by bhavya2269 • 0
0
votes
2
replies
621
views
Question with manipulating OD gene list when running PCA
Pagoda2 PCA RNA-seq Seurat
15 months ago by K • 0
8
votes
5
replies
1.4k
views
Should primary tumor RNA-Seq match their derived cell lines and PDXs? And which dimensionality reduction method should I use?
PDX dimensionality-reduction RNA-Seq PCA
15 months ago by sarahgzb ▴ 40
0
votes
1
reply
618
views
Should genotype PCA in eQTL analysis be performed using all SNPs? or can be with a subset of SNPs?
genotype eQTL SNP PCA
updated 16 months ago by 4.5k • written 16 months ago by ▴ 20
0
votes
0
replies
671
views
Principal component analysis using plotPCA of deepTools
plotpca deeptools pca
17 months ago by Rajendra KC ▴ 20
50 results • Page 1 of 1
Recent Votes
Comment: Comparing whole transcriptome under one condition to the transcriptomes under ot
Comment: Can VST be called Log2 expression in a paper?
Comment: Explanation of DESeq factor leveling
Explanation of DESeq factor leveling
Comment: Run mutltiple Fastq files on Hisat2
filterx : fast and efficient filter tool written in Rust for csv,fasta,fastq,gff,vcf,sam files.
Answer: how to install conda bcftools +fill-tags plugin ?
Recent Locations • All
Germany, just now
Brazil, 5 minutes ago
Macao, 6 minutes ago
UK, 8 minutes ago
China, 12 minutes ago
Sweden, 16 minutes ago
Pakistan, 25 minutes ago
Recent Awards • All
Popular Question to wangziwei0010 ▴ 30
Popular Question to xiaoleiusc ▴ 140
Popular Question to odi ▴ 10
Popular Question to Alewa ▴ 170
Popular Question to Ezequiel ▴ 10
Popular Question to pablo ▴ 310
Popular Question to Jichen Wen ▴ 30
Recent Replies
Answer: Compare Two Sigle-cell Sample for Differentially Expressed Genes (DEGs). How? by ATpoint 85k
> But How could I know if the difference comes from sample instead of sequencing runs or cohort-driven batch effect? You cannot. It's pe…
Comment: Comparing GSEA mutant data to wild type by conmul • 0
Sorry that it was unclear in the post. The data is all CRISPR gene effect scores from DepMap. The 'significant genes' as mentioned in the p…
Comment: How to determine whether it is 10x data by king • 0
Thank you for your answer, it's very inspiring.
Comment: Inquiry about depth of coverage and copy number variation by Chen • 0
Thanks Pierre, I was actually thinking about the duplicate PCR reads and didn't explain it properly. I have found a post mentioning that qu…
Comment: Can a read be aligned more than once? by GenoMax 146k
Yes a read can be aligned more than once (I don't specifically know about gam/gaf). It would be called a "multi-mapping" read. You could im…
Comment: Statistical test to be used for dataset by allingt • 0
The choice of test depends on the types of variables involved and the hypothesis you have. But most importantly on the question you want am…
Comment: dittoHeatmap; adding column labels on the heatmap by jared.andrews07 ★ 18k
I'd consider making a [block annotation](https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#block-annotation…
Comment: Comparing GSEA mutant data to wild type by allingt • 0
What do you mean by "significant gene"? How did you perform GSEA and on how did you rank your genes for it? From guesswork I might initiall…
Comment: Genes of Interest in a Multi-Tissue Analysis by allingt • 0
The DESeq2 manual tells us that the object class of vst() output is a subclass of RangedSummarizedExperiment. I suspect the methods applica…
Comment: WGCNA: Why are my brown, yellow, and other modules not visible in the gene dendr by allingt • 0
Did you perform blockwise module detection by any chance? Are your results object's contents sorted in blocks?
Comment: Why does WGCNA use weighted correlation instead of Pearson correlation? by allingt • 0
The WGCNA implementation by Langfelder and Horvath provides various correlation methods to create the initial correlation matrix. I don't t…
Comment: dittoHeatmap; adding column labels on the heatmap by Varun Gupta ★ 1.3k
any idea, how can I display the labels Pre and POst on the top of the heatmap? I am looking at complexheatmap package as to how they displa…
Comment: How can I determine the p-value of genes within each identified module in WGCNA? by allingt • 0
What p-value do you mean? When and how did you calculate it?
Answer: What is a genomic range that would almost always get decent WGS coverage but is by i.sudbery 20k
What about some of the well known enhancer regions, the globin locus LCR? Likely to be highly sequenceable, and yet not on exome panels.
Answer: Using NumReads column of quants.genes.sf file to build DESeq2 input by i.sudbery 20k
One of the improvements that the using the `salmon` -> `tximport` -> `DESeq2` pipeline, over just a `counts`->`DESeq2` pipeline is the abil…
Traffic: 1606 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6