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0
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375
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Comment: Comment: differential gene expression analysis when not all samples have an untreated cou
8 days ago by nhaus ▴ 310
2
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2
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375
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differential gene expression analysis when not all samples have an untreated counterpart
differential-expression edgeR
8 days ago by nhaus ▴ 310
0
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0
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107
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Surrogate variable analysis for paired RNA seq experiment
sva rnaseq ruvseq
15 days ago by nhaus ▴ 310
1
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1
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301
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Answer: Answer: Analyzing dataset with counts and TMM values?
9 weeks ago by nhaus ▴ 310
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0
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288
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Comment: Comment: pseudobulk differential expression design matrix
9 weeks ago by nhaus ▴ 310
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0
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288
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Comment: Comment: pseudobulk differential expression design matrix
9 weeks ago by nhaus ▴ 310
0
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3
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288
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pseudobulk differential expression design matrix
pseudobulk single-cell scRNA-seq
9 weeks ago by nhaus ▴ 310
0
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0
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273
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Correcting for covariates in GWAS studies and differential gene expression analysis
batch-correction GWAS
updated 6 months ago by 43k • written 6 months ago by ▴ 310
0
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1
reply
606
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GSA type of input data
vst GSEA DESeq2
updated 16 months ago by ★ 7.0k • written 16 months ago by ▴ 310
0
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1
reply
463
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Quantifying GFP and GAL4 reads in drosophila
salmon qunatification read
updated 18 months ago by 11k • written 18 months ago by ▴ 310
0
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0
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729
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Answer: Answer: How to replace Gene Symbols with Ensembl ID?
18 months ago by nhaus ▴ 310
1
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0
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380
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Libtype differs for all samples although same library preparation
salmon rnaseq libtype
18 months ago by nhaus ▴ 310
1
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1
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2.8k
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Comment: Comment: DESeq2 design formula considerations
18 months ago by nhaus ▴ 310
6
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6
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2.8k
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DESeq2 design formula considerations
differential RNAseq expression analysis DGE DESeq2
updated 18 months ago by 4.2k • written 18 months ago by ▴ 310
1
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1
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835
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Comment: Comment: gvcf to bam or fastq
18 months ago by nhaus ▴ 310
0
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0
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1.6k
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Comment: Comment: Tuning seurat integration strength to prevent overcorrection
19 months ago by nhaus ▴ 310
0
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1
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1.6k
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Comment: Comment: Tuning seurat integration strength to prevent overcorrection
19 months ago by nhaus ▴ 310
0
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4
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1.6k
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Tuning seurat integration strength to prevent overcorrection
scRNA seurat
19 months ago by nhaus ▴ 310
2
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1
reply
568
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Answer: Answer: fasta file parsing
20 months ago by nhaus ▴ 310
0
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3
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870
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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 ▴ 310
0
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0
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870
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Comment: Comment: Function/Package which shows how cells correspond to one another between UMAPs
21 months ago by nhaus ▴ 310
3
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2
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705
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Why do highly expressed genes vary more than lowly expressed genes?
single cell statistics
updated 12 months ago by • 0 • written 21 months ago by ▴ 310
0
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0
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1.1k
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Comment: Comment: Using Leiden algorithm to cluster bulk RNA samples
2.1 years ago by nhaus ▴ 310
4
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2
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1.1k
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Using Leiden algorithm to cluster bulk RNA samples
clustering RNAseq Leiden
2.1 years ago by nhaus ▴ 310
2
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1
reply
499
views
How to check if a certain phenotype is over-represented in a cluster
cluster overrepresentation
updated 2.1 years ago by 27k • written 2.1 years ago by ▴ 310
1
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1
reply
907
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Answer: Answer: Equipment for bioinformatics.
2.1 years ago by nhaus ▴ 310
0
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0
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2.1k
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Comment: Comment: plink2 tell "--glm" to use dosage instead of hardcalls
2.1 years ago by nhaus ▴ 310
0
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1
reply
893
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 ▴ 310
2
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2
replies
1.3k
views
Finemapping - how to define a locus?
finemapping locus
updated 2.2 years ago by • 0 • written 2.8 years ago by ▴ 310
2
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1
reply
952
views
Comment: Comment: differential expression RNASeq DESeq2
2.2 years ago by nhaus ▴ 310
3
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1
reply
952
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Answer: Answer: differential expression RNASeq DESeq2
2.2 years ago by nhaus ▴ 310
0
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0
replies
302
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Relate longitudinal measurement of quantitative variable with gene expression data
RNA-seq longitudinal
2.2 years ago by nhaus ▴ 310
0
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1
reply
503
views
Expression of genes in KEGG pathway
KEGG over representation analysis
updated 2.2 years ago by 11k • written 2.2 years ago by ▴ 310
0
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0
replies
363
views
Tools to visualize 2D RNA Heterodimer
visualization RNA
2.2 years ago by nhaus ▴ 310
0
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0
replies
3.2k
views
Answer: Answer: Can anyone share me a good GATK4 workflow
2.5 years ago by nhaus ▴ 310
0
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0
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677
views
Tool: Genotype Imputation Workflow
gwas imputation.
2.6 years ago by nhaus ▴ 310
0
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1
reply
1.4k
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Comment: Comment: Strange speed up in GATK LeftAlignIndels
2.6 years ago by nhaus ▴ 310
15
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2
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2.1k
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Tutorial: Germline variant calling pipeline using Snakemake
snakemake GATK germline_variant_calling
updated 18 months ago by ▴ 830 • written 2.6 years ago by ▴ 310
2
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1
reply
809
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 ▴ 310
0
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0
replies
517
views
Plink genomic inflation estimate
plink inflation genomic GWAS
2.8 years ago by nhaus ▴ 310
1
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3
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2.1k
views
plink2 tell "--glm" to use dosage instead of hardcalls
plink2 gwas imputation
2.1 years ago by nhaus ▴ 310
1
vote
1
reply
2.1k
views
Answer: Answer: plink2 tell "--glm" to use dosage instead of hardcalls
2.8 years ago by nhaus ▴ 310
0
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0
replies
1.4k
views
Minimac4 how is R2 calculated
GWAS minimac4 imputation
2.8 years ago by nhaus ▴ 310
0
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0
replies
1.2k
views
Comment: Comment: IMPUTE2 minimal number of SNPs per chunk
2.8 years ago by nhaus ▴ 310
0
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2
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1.2k
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Comment: Comment: IMPUTE2 minimal number of SNPs per chunk
2.8 years ago by nhaus ▴ 310
2
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6
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1.2k
views
IMPUTE2 minimal number of SNPs per chunk
impute gwas
updated 2.8 years ago by 4.2k • written 2.8 years ago by ▴ 310
0
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1
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612
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IMPUTE2 limit to only one population of 1000G Reference
GWAS impute 1000g
updated 2.8 years ago by 4.2k • written 2.8 years ago by ▴ 310
0
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0
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613
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maxT permutation in plink
plink gwas
2.8 years ago by nhaus ▴ 310
0
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0
replies
856
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Comment: Comment: Why are there nucleotides in the reference genome which are also minor alleles i
2.8 years ago by nhaus ▴ 310
2
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4
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856
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Why are there nucleotides in the reference genome which are also minor alleles in the 1000 genomes project
reference genotype minor allele
updated 2.8 years ago by 47k • written 2.8 years ago by ▴ 310
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