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2
votes
2
replies
1.9k
views
JoinLayers to find markers in merged or integrated analysis in seurat
scRNA-seq seurat FindMarkers
3 months ago by mohammedtoufiq91 ▴ 250
2
votes
4
replies
1.1k
views
How to remove the analysis slots added to my scRNA-Seq and scATAC-Seq data objects in R?
scrna-seq seurat signac
4 months ago by mohammedtoufiq91 ▴ 250
4
votes
2
replies
1.2k
views
How to retrieve Microarray probe annotations
org.Hs.eg.db annotables AnnotationDbi Microarray R
14 months ago by mohammedtoufiq91 ▴ 250
2
votes
3
replies
1.8k
views
Issues marking genes in ComplexHeatmap
pheatmap complexheatmap heatmap ggplot2 R
14 months ago by mohammedtoufiq91 ▴ 250
7
votes
9
replies
1.3k
views
Question about RNA-Seq data alignment
STAR Alignment BBMAP RNA-Seq Bowtie
15 months ago by mohammedtoufiq91 ▴ 250
5
votes
3
replies
818
views
How to map and annotate gene symbols to gene type?
Ensembl RefSeq UCSC biomart RNA-Seq
updated 15 months ago by 142k • written 15 months ago by ▴ 250
2
votes
4
replies
1.4k
views
Unable to run RSEM because of error rsem-parse-alignments : No such file or directory
RNA-Seq Bowtie2 RSEM Boost
16 months ago by mohammedtoufiq91 ▴ 250
0
votes
0
replies
508
views
How to identify mitochondrial contamination in RNAseq and QC data?
QC FastQC MultiQC alignment rna-seq
17 months ago by mohammedtoufiq91 ▴ 250
5
votes
4
replies
1.7k
views
Possibility of marking genes of interest by in ComplexHeatmap
heatmap ggplot2 R complexheatmap
17 months ago by mohammedtoufiq91 ▴ 250
2
votes
2
replies
1.3k
views
Plot heatmap by average based on sample groups
pheatmap complexheatmap heatmap ggplot2 R
17 months ago by mohammedtoufiq91 ▴ 250
1
vote
0
replies
330
views
How to find miRNAs targeting genes using a list in R?
PicTar miRBase miRNA PITA R
17 months ago by mohammedtoufiq91 ▴ 250
1
vote
1
reply
833
views
Representation of variables in PCA
ggplot2 biplot R pcatools pca
updated 20 months ago by ▴ 520 • written 20 months ago by ▴ 250
5
votes
2
replies
2.9k
views
How to adjust font size of row_split labels in ComplexHeatmap R package
Heatmap ComplexHeatmap R labels
updated 23 months ago by 21k • written 23 months ago by ▴ 250
1
vote
3
replies
1.6k
views
Help with plotting heatmap with both row and column label annotations
pheatmap ComplexHeatmap R Heatmap annotations
updated 23 months ago by ★ 1.8k • written 23 months ago by ▴ 250
5
votes
5
replies
1.3k
views
Extraction of high variance or contributing genes using pcatools
PCAtools FactoMineR R prcomp PCA
23 months ago by mohammedtoufiq91 ▴ 250
4
votes
3
replies
757
views
How to label genes passing the p-value and fold change cut-offs in EnhancedVolcano?
EnhancedVolcano volcano label R genes
updated 2.1 years ago by 142k • written 2.1 years ago by ▴ 250
5
votes
4
replies
1.1k
views
Unable to open pdf file of volcano plots created using many group comparisons from EnhancedVolcano package in R
tidyverse forloops EnhancedVolcano volcano R
2.1 years ago by mohammedtoufiq91 ▴ 250
2
votes
2
replies
1.2k
views
Error in ComplexHeatmap while adding barplot as column annotations
ComplexHeatmap heatmap barplot R annotation
2.1 years ago by mohammedtoufiq91 ▴ 250
6
votes
4
replies
4.2k
views
How to add color scheme for many groups in PCA using R?
R biplot PCA PCAtools ggplot2
2.3 years ago by mohammedtoufiq91 ▴ 250
6
votes
4
replies
1.5k
views
Batch effect correction: Input data format for removeBatchEffect from limma package
R effects limma batch removeBatchEffect
updated 2.4 years ago by ★ 7.2k • written 2.4 years ago by ▴ 250
2
votes
4
replies
7.9k
views
Error while running PCAtools (Error in svd(x, nu = nu, nv = nv) : infinite or missing values in 'x')
missMDA R PCAtools PCA
updated 11 months ago by 43k • written 2.4 years ago by ▴ 250
0
votes
1
reply
738
views
Combining Microarray and RNA-Seq datasets visualization and comparison
ComBat microarray sva RNAseq expression gene
updated 2.4 years ago by 82k • written 2.4 years ago by ▴ 250
2
votes
2
replies
2.6k
views
Exporting normalized counts data from DeSeq2
DESeq2 normalization expression RNA-seq
updated 20 months ago by 43k • written 2.7 years ago by ▴ 250
1
vote
2
replies
1.3k
views
Combining RNA-Seq read counts from 2 lanes of the same sample (.txt file)
expression featurecounts counts rna-seq gene
2.7 years ago by mohammedtoufiq91 ▴ 250
4
votes
5
replies
1.5k
views
Calculate fold change in edgeR with one sample per condition
R edgeR expression rna-seq differential
2.7 years ago by mohammedtoufiq91 ▴ 250
8
votes
6
replies
4.3k
views
How to convert log2 scale RNA-Seq expression data to linear scale data
expression edgeR R rna-seq fold-change
updated 2.7 years ago by 13k • written 2.7 years ago by ▴ 250
9
votes
7
replies
2.8k
views
Averaging duplicates of a gene in RNA-Seq dataset
expression differential average R rna-seq
updated 2.8 years ago by ▴ 60 • written 2.9 years ago by ▴ 250
2
votes
4
replies
1.0k
views
How to create gene level data from a probe level data?
R sum mean gene microarray
2.9 years ago by mohammedtoufiq91 ▴ 250
1
vote
2
replies
729
views
How to calculate the difference between the RNA-Seq individual samples?
comparison expression edgeR replicates R
2.9 years ago by mohammedtoufiq91 ▴ 250
1
vote
1
reply
499
views
Flooring (adjusting) values in Gene Expression Microarray data analysis?
gene-expression microarray R
updated 3.0 years ago by 82k • written 3.0 years ago by ▴ 250
0
votes
1
reply
2.9k
views
How to increase the size of the top annotation bars in Complexheatmap
plot annotation ComplexHeatmap heatmap
3.1 years ago by mohammedtoufiq91 ▴ 250
1
vote
5
replies
1.3k
views
How to sort multi columns on long dataframe in R
data.frame Order R dplyr plyr
updated 3.1 years ago by ▴ 140 • written 3.1 years ago by ▴ 250
4
votes
4
replies
2.4k
views
Customize fold change legend values in ComplexHeatmap
ComplexHeatmap circlize colorRamp2 R matrix
updated 3.4 years ago by 20 • written 3.6 years ago by ▴ 250
6
votes
5
replies
5.1k
views
How to visualize Boxplot with using fold change values in ggplot2 in R
Boxplot ggplot2 R fold change
updated 3.8 years ago by 13k • written 3.8 years ago by ▴ 250
1
vote
5
replies
2.8k
views
Batch effect identification using PCA
PCA qRT-PCR R targeted-assay Batch-Effect
updated 4 weeks ago by 43k • written 3.9 years ago by ▴ 250
1
vote
5
replies
1.5k
views
PCA plot on genes and color by batch and plate information
pca factoextra ggfortify ggplot2 reshape2
3.9 years ago by mohammedtoufiq91 ▴ 250
3
votes
5
replies
1.9k
views
Unable to locate libraries in latest version of R 4.0.0
R library missing r studio installation
updated 4.0 years ago by 20 • written 4.0 years ago by ▴ 250
2
votes
5
replies
2.4k
views
Error while using ComplexHeatmap
R data.frame ComplexHeatmap heatmap clustering
4.0 years ago by mohammedtoufiq91 ▴ 250
0
votes
1
reply
1.5k
views
How to combine different data types and perform PCA in R
PCA Microarray RNA-Seq data frame R
4.0 years ago by mohammedtoufiq91 ▴ 250
7
votes
6
replies
1.0k
views
Error while plotting in ggplot2
ggplot2 data.frame grid plot geom_point
updated 4.1 years ago by 43k • written 4.1 years ago by ▴ 250
1
vote
2
replies
5.0k
views
Plotting multiple line plots using ggplot2 and save as pdf
ggplot2 r cowplot lineplot
updated 4.3 years ago by 20 • written 4.5 years ago by ▴ 250
0
votes
0
replies
1.1k
views
How to plot boxplot on two variables in ggplot2
boxplot ggplot2 variables reshape2 R
4.3 years ago by mohammedtoufiq91 ▴ 250
4
votes
2
replies
3.1k
views
Add borders to the shapes in the PCA plot by using autoplot
ggfortify R PCA autoplot ggplot2
updated 4.3 years ago by 11k • written 4.3 years ago by ▴ 250
4
votes
3
replies
7.6k
views
How to plot variables in ggplot2 based on color by value
R ggplot2 geom_point variable dataframe
4.3 years ago by mohammedtoufiq91 ▴ 250
10
votes
4
replies
4.2k
views
How to plot PCA on two or more variables
pca3d FactoMineR R PCA variables
4.5 years ago by mohammedtoufiq91 ▴ 250
9
votes
13
replies
4.0k
views
How to adjust and align timepoints on x-axis in the ggplot2
ggplot2 r line plot x-axis data frame
updated 4.5 years ago by 11k • written 4.5 years ago by ▴ 250
3
votes
6
replies
7.9k
views
Plotting a line graph using the ggplot2 for multiple columns (genes)
ggplot2 line graph R
updated 4.5 years ago by 43k • written 4.5 years ago by ▴ 250
1
vote
3
replies
1.1k
views
Imputation of missing values for RT-qPCR data
missmda missing values impute RT-qPCR heatmap
4.5 years ago by mohammedtoufiq91 ▴ 250
4
votes
2
replies
1.3k
views
Error while using ComplexHeatmap
ComplexHeatmap missing values R library
4.5 years ago by mohammedtoufiq91 ▴ 250
0
votes
2
replies
1.2k
views
Mapping common identifiers between two files
merge mapping csv R
4.5 years ago by mohammedtoufiq91 ▴ 250
75 results • Page 1 of 2
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