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16
votes
11
replies
8.4k
views
DESeq2 design with multiple conditions
DESeq2
updated 16 months ago by 43k • written 4.6 years ago by ▴ 250
0
votes
1
reply
656
views
error running popularvote - popv
TabulaSapiens popularVote popv celllabeling
21 months ago by maria2019 ▴ 250
6
votes
10
replies
6.5k
views
7 follow
Strange MT% in 10X scRNA-seq data analysis
Seurat 10X scRNA-seq MT%
updated 2.2 years ago by • 0 • written 5.0 years ago by ▴ 250
0
votes
2
replies
806
views
how to add a config file to docker
docker container offtopic
updated 2.3 years ago by 43k • written 2.3 years ago by ▴ 250
1
vote
4
replies
1.5k
views
Including tbi file along with VCF when running VEP on remote dataset (GnomadV3)
VCF VEP gnomad annotation
2.4 years ago by maria2019 ▴ 250
2
votes
6
replies
1.6k
views
How to iterate over all elements of a dataframe and make changes based on a function
function R datafram
2.4 years ago by maria2019 ▴ 250
1
vote
2
replies
883
views
Adding new samples to single cell rna-seq analysis
batch scRNA-seq seurat
3.0 years ago by maria2019 ▴ 250
0
votes
1
reply
2.5k
views
How to chose best ligand option based on affinity and RMSD from Autodock vina docking results?
RMSD Autodock vina docking binding affinity ligand
updated 3.6 years ago by ▴ 10 • written 3.8 years ago by ▴ 250
0
votes
0
replies
937
views
Why Grid centers are different between Glide and ADTvina for the same Ligand-protein structures
docking vina glide grid Autodock vina
3.8 years ago by maria2019 ▴ 250
1
vote
2
replies
1.0k
views
how to analyze/integrate methylation "beta value" and RNA-seq "FPKM" data from only one cell line
omics integration RNA-seq FPKM beta value
3.8 years ago by maria2019 ▴ 250
1
vote
1
reply
1.6k
views
Which journals accept molecular docking analysis using Autodock vina
autodock vina molecular docking ligand journal
updated 4.0 years ago by ★ 27k • written 4.0 years ago by ▴ 250
1
vote
2
replies
1.5k
views
Zinc data base drug ID to drug name convertor
ID to name Zinc database drug name
updated 4.1 years ago by ★ 27k • written 4.1 years ago by ▴ 250
0
votes
1
reply
853
views
how to get methylated fragments (CpG regions) for only ONE sample using DMAP
Dmap DMR methylation CpG
updated 2.3 years ago by ▴ 130 • written 4.2 years ago by ▴ 250
2
votes
3
replies
2.1k
views
Why the PCA results of PCASamples() from methylkit is different from prcomp()?
methylkit prcomp pca PCASamples multiplePCA
updated 12 days ago by ★ 1.2k • written 4.2 years ago by ▴ 250
3
votes
2
replies
2.7k
views
How to generate CpG REGIONs file to run DMR analysis with methylkit?
DMR methylkit CpG-regions RRBS
updated 4.2 years ago by 8.2k • written 4.2 years ago by ▴ 250
1
vote
4
replies
11k
views
How to plot 2 different symbols in a 3D PCA plot generated by rgl-plot3D
3D_PCA rgl plot3D rna-seq
4.2 years ago by maria2019 ▴ 250
10
votes
5
replies
5.1k
views
Why do I get different results for PC1 from plotPCA(DESeq2) and prcomp?
plotPCA deseq2 prcomp PCA
4.3 years ago by maria2019 ▴ 250
0
votes
2
replies
3.3k
views
What is the best R package to plot eye catching 3D PCA plots?
PCA plot R
4.3 years ago by maria2019 ▴ 250
3
votes
13
replies
1.2k
views
statistics method to find the relation between multiple variables of 50 samples
statistics
updated 4.3 years ago by 20 • written 4.3 years ago by ▴ 250
1
vote
2
replies
847
views
Is it logical to compare the expression FPKM with the percent methylation data at genes?
RNA-Seq methylation expression-methylation counts
4.3 years ago by maria2019 ▴ 250
0
votes
0
replies
1.0k
views
Integration analysis of atac-seq, rna-seq, and methylation data at specific gene regions
atac-seq RNA-Seq methylation Integration_Analysis
4.3 years ago by maria2019 ▴ 250
5
votes
2
replies
1.1k
views
How to plot gene_names besides CpGs in microarray methylation heatmap?
limma Differential CpG microarray heatmap.2
4.3 years ago by maria2019 ▴ 250
2
votes
1
reply
793
views
How to calculate methylation FC for genes based on CpG FC data?
methylation fold-change
updated 4.3 years ago by 104k • written 4.3 years ago by ▴ 250
4
votes
2
replies
1.1k
views
How to remove spike ins from illumina beadchip data
microarray limma beadchip illumina ERCC
updated 4.3 years ago by 87k • written 4.3 years ago by ▴ 250
4
votes
2
replies
1.0k
views
Error in inputting multiple illumina microarray idat files to limma
R idat limma microarray
updated 4.3 years ago by ★ 7.0k • written 4.3 years ago by ▴ 250
3
votes
4
replies
1.4k
views
RRBS analysis using methylkit with 2 variables
methylkit RRBS DMR
4.4 years ago by maria2019 ▴ 250
2
votes
2
replies
1.3k
views
miRNA fastqc sequence length distribution with UMI
miRNA fastqc cutadapt trimming Qiagene
updated 4.5 years ago by 14k • written 4.5 years ago by ▴ 250
3
votes
2
replies
2.0k
views
why my WGS bam file (after alignment) shows more reads than the starting fastq file
WGS fastqc qualimap QC total read
4.5 years ago by maria2019 ▴ 250
5
votes
11
replies
1.9k
views
Can I filter mRNA from bulk RNA-seq reads?
mRNA-seq bulk RNA-seq
updated 4.5 years ago by ▴ 160 • written 4.5 years ago by ▴ 250
16
votes
6
replies
2.8k
views
Batch effect problem DEG, DESseq2
DESeq2 batch-effect RNA-seq DEG
updated 5 months ago by 81k • written 4.6 years ago by ▴ 250
7
votes
6
replies
2.9k
views
Detecting outlier DESeq2
deseq2 pca DEG bulk RNA-seq
updated 4.6 years ago by 87k • written 4.6 years ago by ▴ 250
2
votes
3
replies
2.4k
views
order of trimming for RNA-seq QC
RNA-Seq cutadapt QC fastQC
5.0 years ago by maria2019 ▴ 250
7
votes
4
replies
1.0k
views
Can you use germline variation calling on a normal embryonic stem cell line?
SNP WES embryonic cell germline variation GATK
updated 5.1 years ago by 23k • written 5.1 years ago by ▴ 250
0
votes
6
replies
2.1k
views
why does qualimap2 shows different results for number of mismatches for bowtie2 and BWAMEM?
WES qualimap bowtie2 bwamem
updated 5.1 years ago by 35k • written 5.1 years ago by ▴ 250
0
votes
1
reply
1.2k
views
Should I use the same reference indexing command of bwa for WGS and WES analysis?
bwa mem indexing WGS WES
updated 5.1 years ago by 16k • written 5.1 years ago by ▴ 250
0
votes
1
reply
1.1k
views
How many SNPs I should expect to see in a normal human embryonic stem cell (hESC) with WES analysis?
SNP hESC WES samtools
5.1 years ago by maria2019 ▴ 250
3
votes
6
replies
23k
views
6 follow
What is the right illumina universal adapter sequence for trimming paired-end reads?
WES fastqc trimadaptor
updated 5.1 years ago by 5.8k • written 5.1 years ago by ▴ 250
3
votes
2
replies
1.9k
views
Does strange fastQC GC content report cause a problem for WES analysis?
fastQC WES GC content
updated 5.1 years ago by 13k • written 5.1 years ago by ▴ 250
2
votes
5
replies
1.2k
views
Should I specify exome region to do the QC with qualimap2 for WES analysis?
qualimap2 WES QC
updated 5.1 years ago by 35k • written 5.1 years ago by ▴ 250
39 results • Page 1 of 1
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