Profile Posts Awards
Show
all questions tools blogs news tutorials forum answers comments
Showing : questions
2
votes
2
replies
432
views
differential gene expression analysis when not all samples have an untreated counterpart
differential-expression edgeR
29 days ago by nhaus ▴ 360
0
votes
0
replies
118
views
Surrogate variable analysis for paired RNA seq experiment
sva rnaseq ruvseq
5 weeks ago by nhaus ▴ 360
0
votes
3
replies
342
views
pseudobulk differential expression design matrix
pseudobulk single-cell scRNA-seq
12 weeks ago by nhaus ▴ 360
0
votes
0
replies
282
views
Correcting for covariates in GWAS studies and differential gene expression analysis
batch-correction GWAS
updated 7 months ago by 43k • written 7 months ago by ▴ 360
0
votes
1
reply
621
views
GSA type of input data
vst GSEA DESeq2
updated 16 months ago by ★ 7.2k • written 16 months ago by ▴ 360
0
votes
1
reply
477
views
Quantifying GFP and GAL4 reads in drosophila
salmon qunatification read
updated 18 months ago by 11k • written 18 months ago by ▴ 360
1
vote
0
replies
384
views
Libtype differs for all samples although same library preparation
salmon rnaseq libtype
18 months ago by nhaus ▴ 360
6
votes
6
replies
3.0k
views
DESeq2 design formula considerations
differential RNAseq expression analysis DGE DESeq2
updated 18 months ago by 4.2k • written 19 months ago by ▴ 360
0
votes
4
replies
1.7k
views
Tuning seurat integration strength to prevent overcorrection
scRNA seurat
20 months ago by nhaus ▴ 360
0
votes
3
replies
886
views
Function/Package which shows how cells correspond to one another between UMAPs
scRNAseq visualization
updated 21 months ago by 82k • written 21 months ago by ▴ 360
3
votes
2
replies
725
views
Why do highly expressed genes vary more than lowly expressed genes?
single cell statistics
updated 13 months ago by • 0 • written 22 months ago by ▴ 360
4
votes
2
replies
1.2k
views
Using Leiden algorithm to cluster bulk RNA samples
clustering RNAseq Leiden
2.1 years ago by nhaus ▴ 360
2
votes
1
reply
511
views
How to check if a certain phenotype is over-represented in a cluster
cluster overrepresentation
updated 2.2 years ago by 27k • written 2.2 years ago by ▴ 360
0
votes
1
reply
915
views
What to do if covariates in design matrix of limma are confounded
gene expression differential limma
updated 2.2 years ago by 82k • written 2.2 years ago by ▴ 360
2
votes
2
replies
1.4k
views
Finemapping - how to define a locus?
finemapping locus
updated 2.3 years ago by • 0 • written 2.8 years ago by ▴ 360
0
votes
0
replies
306
views
Relate longitudinal measurement of quantitative variable with gene expression data
RNA-seq longitudinal
2.3 years ago by nhaus ▴ 360
0
votes
1
reply
514
views
Expression of genes in KEGG pathway
KEGG over representation analysis
updated 2.3 years ago by 11k • written 2.3 years ago by ▴ 360
0
votes
0
replies
366
views
Tools to visualize 2D RNA Heterodimer
visualization RNA
2.3 years ago by nhaus ▴ 360
2
votes
1
reply
823
views
command line VEP and VEP web interface return different results.
ensembl vep
updated 2.8 years ago by 23k • written 2.8 years ago by ▴ 360
0
votes
0
replies
522
views
Plink genomic inflation estimate
plink inflation genomic GWAS
2.8 years ago by nhaus ▴ 360
1
vote
3
replies
2.1k
views
plink2 tell "--glm" to use dosage instead of hardcalls
plink2 gwas imputation
2.2 years ago by nhaus ▴ 360
0
votes
0
replies
1.4k
views
Minimac4 how is R2 calculated
GWAS minimac4 imputation
2.9 years ago by nhaus ▴ 360
2
votes
6
replies
1.2k
views
IMPUTE2 minimal number of SNPs per chunk
impute gwas
updated 2.9 years ago by 4.2k • written 2.9 years ago by ▴ 360
0
votes
1
reply
620
views
IMPUTE2 limit to only one population of 1000G Reference
GWAS impute 1000g
updated 2.9 years ago by 4.2k • written 2.9 years ago by ▴ 360
0
votes
0
replies
621
views
maxT permutation in plink
plink gwas
2.9 years ago by nhaus ▴ 360
2
votes
4
replies
868
views
Why are there nucleotides in the reference genome which are also minor alleles in the 1000 genomes project
reference genotype minor allele
updated 2.9 years ago by 47k • written 2.9 years ago by ▴ 360
1
vote
1
reply
1.1k
views
What happens to the genotype field in a g.vcf after CombineGVCFs
GT GATK CombineGVCFs genotype
updated 2.9 years ago by ▴ 20 • written 3.0 years ago by ▴ 360
2
votes
3
replies
1.9k
views
Ambiguous SNPs
SNPs
updated 2.9 years ago by 23k • written 2.9 years ago by ▴ 360
0
votes
0
replies
430
views
Illumina Omni2.5 genotyping get actual genotypes.
genotyping omni illumina
3.0 years ago by nhaus ▴ 360
2
votes
5
replies
1.3k
views
SHAPEIT v4 modify keep QUAL FORMAT and INFO field
shapeit phasing haplotype
3.0 years ago by nhaus ▴ 360
1
vote
3
replies
1.4k
views
GATK ApplyVQSR filtering doesnt work
gatk variant calling germline
3.0 years ago by nhaus ▴ 360
1
vote
5
replies
1.9k
views
Liftover vcf file from hs37d5 assembly to b37 assembly
vcf liftover assembly
updated 2.7 years ago by ▴ 90 • written 3.0 years ago by ▴ 360
5
votes
2
replies
1.3k
views
High confident germline SNP and INDELS for VQSR for reference genome GRCh37
INDEL SNP 1000g GRCh37
3.0 years ago by nhaus ▴ 360
0
votes
1
reply
672
views
Predicting Drug responds from somatic mutations
prediction somatic responds drug
updated 3.0 years ago by ▴ 570 • written 3.0 years ago by ▴ 360
1
vote
4
replies
1.5k
views
Create Mutational signature plot from vcf file.
R python mutational
3.1 years ago by nhaus ▴ 360
3
votes
5
replies
790
views
conceptual question about paired end sequencing
sequencing illumina
updated 3.2 years ago by 43k • written 3.2 years ago by ▴ 360
4
votes
5
replies
3.3k
views
VEP is very slow. Fork doesnt seem to work
vep annotation
3.0 years ago by nhaus ▴ 360
0
votes
1
reply
817
views
Experience with BaseRecalibratorSpark and ApplyBQSRSpark
gatk somatic mutations snp
updated 3.2 years ago by 6.4k • written 3.2 years ago by ▴ 360
0
votes
0
replies
880
views
Panel of normals for Mutect2 GRCh37
gatk broad mutect2
3.3 years ago by nhaus ▴ 360
1
vote
5
replies
892
views
biomaRt external_gene_name same entry multiple times when mapping to homolog mouse gene
ensembl mapping homology
3.3 years ago by nhaus ▴ 360
0
votes
0
replies
424
views
chi-square test to identify significantly mutated genes
genome sequencing
3.3 years ago by nhaus ▴ 360
0
votes
4
replies
1.3k
views
Duplicated genes in overrepresentation analysis (ORA)
ORA GSEA
updated 3.3 years ago by ▴ 200 • written 3.3 years ago by ▴ 360
0
votes
0
replies
445
views
Proper way of comparing list of mutated genes
gene GSEA
3.3 years ago by nhaus ▴ 360
3
votes
3
replies
1.0k
views
Count, LT, PH, PT Column in Functional Annotation Chart of DAVID
DAVID GSEA
updated 3.3 years ago by 10k • written 3.3 years ago by ▴ 360
0
votes
0
replies
642
views
versioned transcripts with SnpEff GRCh37
SnpEff annotation
3.4 years ago by nhaus ▴ 360
2
votes
2
replies
879
views
GT 0/0 in VCF file
genome
3.4 years ago by nhaus ▴ 360
0
votes
3
replies
634
views
Using StringTie with CAGE-seq data
StringTie
3.7 years ago by nhaus ▴ 360
0
votes
5
replies
2.6k
views
Merging BAM vs concatenate FASTQ
sequencing genome
3.7 years ago by nhaus ▴ 360
4
votes
9
replies
2.9k
views
Questions about reference genome and alignment
genome alignment assembly
updated 3.8 years ago by 13k • written 3.8 years ago by ▴ 360
1
vote
1
reply
922
views
How to download BAM file from VM
bam VM
updated 14 months ago by 43k • written 3.9 years ago by ▴ 360
57 results • Page 1 of 2
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