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2
votes
2
replies
560
views
Is MACS3 the same as MACS2?
MACS MACS3 MACS2
updated 3 months ago by 142k • written 3 months ago by ▴ 40
6
votes
5
replies
731
views
Tests for the linear and non-linear relationship between two genes
ode drc correlation regression rnaseq
updated 4 months ago by 82k • written 4 months ago by ▴ 40
0
votes
1
reply
376
views
Testing the interaction term in single-cell RNAseq DEG analysis
DEG scRNAseq Seurat
updated 6 months ago by 82k • written 6 months ago by ▴ 40
0
votes
7
replies
1.2k
views
Highly inflated p-values in GWAS by regenie
regenie plink gwas
7 months ago by cwwong13 ▴ 40
2
votes
7
replies
866
views
Should we assume UMI-based scRNAseq data is not compositional?
compositional scRNAseq
9 months ago by cwwong13 ▴ 40
0
votes
1
reply
520
views
Is it proper to compare two WGCNA matrixes if they were raised to different power (soft threshold)?
WGCNA r RNA-seq cluster
updated 9 months ago by 43k • written 9 months ago by ▴ 40
0
votes
3
replies
784
views
Summarizing permutation test/ bootstrap result for multiple samples for single-cell RNAseq data
single-cell RNA-seq
13 months ago by cwwong13 ▴ 40
0
votes
1
reply
501
views
overlay ggplot graphs like those merging channels in imagej
ggplot imagej
updated 14 months ago by 3.9k • written 14 months ago by ▴ 40
1
vote
0
replies
463
views
What are the differences between GSVA and ssGSEA (in layman's term)?
ssGSEA GSVA GSEA
14 months ago by cwwong13 ▴ 40
3
votes
4
replies
784
views
Do I need to adjust the pvalue if I am only going to test one gene from omics data containing many genes?
pvalue Omics RNAseq
14 months ago by cwwong13 ▴ 40
2
votes
2
replies
684
views
List of genes that are uniquely found in human (not in mouse)
orthologue genome gene
updated 17 months ago by 43k • written 17 months ago by ▴ 40
0
votes
1
reply
811
views
Is it possible to infer whether a patient is with homozygous with the alternative alleles (at two different location)
association WES variant genome
updated 23 months ago by ★ 2.9k • written 2.8 years ago by ▴ 40
2
votes
3
replies
1.1k
views
Determine sex/ gender of a mouse cell line via sequencing data
sequencing line cell
updated 22 months ago by ▴ 120 • written 24 months ago by ▴ 40
1
vote
10
replies
2.1k
views
The modules are not clustered together after WGCNA
cluster WGCNA r dendrograms
2.0 years ago by cwwong13 ▴ 40
2
votes
1
reply
716
views
Ways or packages to analyze single-cell RNAseq data that prepared following Tang's protocol
cell RNAseq seurat single
updated 2.1 years ago by 82k • written 2.1 years ago by ▴ 40
1
vote
3
replies
833
views
What is the current recommended way to process/ analyze Ion Torrent Proton RNAseq data
RNAseq Proton Ion analysis Torrent pipeline processing
updated 2.2 years ago by 100k • written 2.2 years ago by ▴ 40
0
votes
3
replies
921
views
COVID-19 WGS sequencing for individuals having mRNA vaccination
mRNA COVID vaccine WGS
updated 2.4 years ago by 11k • written 2.4 years ago by ▴ 40
0
votes
0
replies
503
views
Molecular docking considerations
binding affinity vina biology docking structural ligand
2.5 years ago by cwwong13 ▴ 40
4
votes
4
replies
2.0k
views
Proper way(s) to perform enrichment analysis in R
GSEA analysis enrichment R RNAseq
updated 2.6 years ago by ▴ 90 • written 2.6 years ago by ▴ 40
2
votes
4
replies
4.1k
views
normalization to "housekeeping" genes of RNAseq data vs qPCR result
qPCR RNAseq
updated 2.7 years ago by 82k • written 2.7 years ago by ▴ 40
0
votes
3
replies
984
views
Assessing how similar/ different of activated pathways between multiple groups of samples
pathway correlation test hypothesis
updated 2.7 years ago by 4.2k • written 2.7 years ago by ▴ 40
0
votes
0
replies
413
views
assessing relative contribution of samples/ organs towards a diseases in multi-tissue RNAseq
RNAseq
2.7 years ago by cwwong13 ▴ 40
0
votes
1
reply
655
views
Association analysis with SNP
association WGS GWAS SNP WES
updated 2.8 years ago by ▴ 1000 • written 2.8 years ago by ▴ 40
0
votes
2
replies
694
views
program/ software to generate large synthetic benchmark gene/ protein interaction network
PPI interaction benchmark network R
2.8 years ago by cwwong13 ▴ 40
2
votes
6
replies
1.5k
views
sequencing adapter/ index when mixing two library preparation kit
adapter RNA-Seq illumina index
updated 2.8 years ago by 14k • written 2.9 years ago by ▴ 40
0
votes
4
replies
885
views
different padj from DESeq2 when using different contrast input format
DESeq2 RNA-Seq
2.9 years ago by cwwong13 ▴ 40
0
votes
0
replies
613
views
Focused pathway analysis
fgsea clusterProfiler GSEA KEGG pathway
3.0 years ago by cwwong13 ▴ 40
0
votes
1
reply
2.0k
views
how to run and use the ENCODE ATAC-seq pipline
ATAC-seq ENCODE peak
updated 3.0 years ago by 22k • written 3.2 years ago by ▴ 40
0
votes
0
replies
1.9k
views
Troubleshooting abnormal ATAC-seq diagnostic plots
QC Sequencing ATAC-seq Troubleshooting
3.0 years ago by cwwong13 ▴ 40
3
votes
3
replies
1.4k
views
Can I pool RNA-seq library with ATAC-seq library and sequence in the same S4 lane?
RNA-seq Sequencing ATAC-seq
updated 3.1 years ago by 142k • written 3.1 years ago by ▴ 40
0
votes
2
replies
2.0k
views
Is it worth to analyzing low quality ATAC-seq data
ATAC-seq QC TSS
3.1 years ago by cwwong13 ▴ 40
11
votes
5
replies
1.4k
views
Does DESeq2 and EdgeR account for the increased total RNA production in one of the experimental group
RNA-Seq DESeq2 EdgeR
updated 3.2 years ago by 19k • written 3.2 years ago by ▴ 40
0
votes
1
reply
1.0k
views
Confusion of the input format for DESeq2 and EdgeR for bulk- and scRNA-seq
DESeq2 EdgeR RNA-Seq scRNA-seq
3.2 years ago by cwwong13 ▴ 40
0
votes
0
replies
747
views
Getting normalized count/ gene expression matrix for both bulk and single-cell RNA-seq
RNA-Seq scRNA-seq DESeq2 EdgeR
3.2 years ago by cwwong13 ▴ 40
2
votes
3
replies
3.2k
views
R object can allow duplicated column name and storing different types of values
R python
updated 3.2 years ago by 43k • written 3.2 years ago by ▴ 40
1
vote
2
replies
1.6k
views
ATAC-seq bowtie2 alignment and pre-alignment adapter clipping
ATAC-seq alignment bowtie2
updated 3.2 years ago by 82k • written 3.2 years ago by ▴ 40
0
votes
0
replies
767
views
Deseq2 getting ANOVA-like result from 3 by 3 factor design
R RNA-Seq Deseq2 anova
updated 4.0 years ago by 142k • written 4.0 years ago by ▴ 40
0
votes
1
reply
1.8k
views
Calculating coverage of genes which have accounted for multiple best hits from bam/sam files
alignment next-gen bwa samtools bedtools
updated 6.7 years ago by 54k • written 6.7 years ago by ▴ 40
38 results • Page 1 of 1
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