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12
votes
5
replies
947
views
Tutorial: removeBatchEffect explained using base R linear models
removebatcheffects limma batch-effect
updated 21 days ago by ▴ 70 • written 6 months ago by ▴ 420
0
votes
1
reply
396
views
Using Pseudobulk Approach for Identifying Marker Genes Within a Single Condition
differential-expression single-cell pseudobulk
updated 4 months ago by 85k • written 4 months ago by ▴ 420
0
votes
0
replies
203
views
Linear Mixed Model for Differential Gene Expression in Single-Cell RNAseq with Batch Effects
MAST differential-expression lmer
updated 4 months ago by 44k • written 4 months ago by ▴ 420
0
votes
0
replies
500
views
Comment: Comment: Specifying a variable as a random effect in model.matrix()
4 months ago by nhaus ▴ 420
1
vote
2
replies
389
views
Go from protein mutation back to gene mutation
mutations tools
updated 5 months ago by 147k • written 5 months ago by ▴ 420
0
votes
0
replies
650
views
Comment: Comment: differential gene expression analysis when not all samples have an untreated cou
7 months ago by nhaus ▴ 420
2
votes
2
replies
650
views
differential gene expression analysis when not all samples have an untreated counterpart
differential-expression edgeR
7 months ago by nhaus ▴ 420
0
votes
0
replies
219
views
Surrogate variable analysis for paired RNA seq experiment
sva rnaseq ruvseq
7 months ago by nhaus ▴ 420
1
vote
1
reply
471
views
Answer: Answer: Analyzing dataset with counts and TMM values?
9 months ago by nhaus ▴ 420
0
votes
0
replies
537
views
Comment: Comment: pseudobulk differential expression design matrix
9 months ago by nhaus ▴ 420
0
votes
0
replies
537
views
Comment: Comment: pseudobulk differential expression design matrix
9 months ago by nhaus ▴ 420
0
votes
3
replies
537
views
pseudobulk differential expression design matrix
pseudobulk single-cell scRNA-seq
9 months ago by nhaus ▴ 420
0
votes
0
replies
360
views
Correcting for covariates in GWAS studies and differential gene expression analysis
batch-correction GWAS
updated 13 months ago by 44k • written 13 months ago by ▴ 420
0
votes
1
reply
728
views
GSA type of input data
vst GSEA DESeq2
updated 23 months ago by ★ 7.6k • written 23 months ago by ▴ 420
0
votes
1
reply
575
views
Quantifying GFP and GAL4 reads in drosophila
salmon qunatification read
updated 2.1 years ago by 11k • written 2.1 years ago by ▴ 420
0
votes
0
replies
865
views
Answer: Answer: How to replace Gene Symbols with Ensembl ID?
2.1 years ago by nhaus ▴ 420
1
vote
0
replies
442
views
Libtype differs for all samples although same library preparation
salmon rnaseq libtype
2.1 years ago by nhaus ▴ 420
1
vote
1
reply
4.0k
views
Comment: Comment: DESeq2 design formula considerations
2.1 years ago by nhaus ▴ 420
6
votes
6
replies
4.0k
views
DESeq2 design formula considerations
differential RNAseq expression analysis DGE DESeq2
updated 2.1 years ago by 4.5k • written 2.1 years ago by ▴ 420
1
vote
1
reply
1.1k
views
Comment: Comment: gvcf to bam or fastq
2.1 years ago by nhaus ▴ 420
0
votes
0
replies
2.1k
views
Comment: Comment: Tuning seurat integration strength to prevent overcorrection
2.2 years ago by nhaus ▴ 420
0
votes
1
reply
2.1k
views
Comment: Comment: Tuning seurat integration strength to prevent overcorrection
2.2 years ago by nhaus ▴ 420
0
votes
4
replies
2.1k
views
Tuning seurat integration strength to prevent overcorrection
scRNA seurat
2.2 years ago by nhaus ▴ 420
2
votes
1
reply
669
views
Answer: Answer: fasta file parsing
2.2 years ago by nhaus ▴ 420
0
votes
3
replies
997
views
Function/Package which shows how cells correspond to one another between UMAPs
scRNAseq visualization
updated 2.3 years ago by 85k • written 2.3 years ago by ▴ 420
0
votes
0
replies
997
views
Comment: Comment: Function/Package which shows how cells correspond to one another between UMAPs
2.3 years ago by nhaus ▴ 420
3
votes
2
replies
858
views
Why do highly expressed genes vary more than lowly expressed genes?
single cell statistics
updated 19 months ago by • 0 • written 2.3 years ago by ▴ 420
0
votes
0
replies
1.4k
views
Comment: Comment: Using Leiden algorithm to cluster bulk RNA samples
2.6 years ago by nhaus ▴ 420
4
votes
2
replies
1.4k
views
Using Leiden algorithm to cluster bulk RNA samples
clustering RNAseq Leiden
2.6 years ago by nhaus ▴ 420
2
votes
1
reply
604
views
How to check if a certain phenotype is over-represented in a cluster
cluster overrepresentation
updated 2.7 years ago by 27k • written 2.7 years ago by ▴ 420
1
vote
1
reply
1.1k
views
Answer: Answer: Equipment for bioinformatics.
2.7 years ago by nhaus ▴ 420
0
votes
0
replies
2.5k
views
Comment: Comment: plink2 tell "--glm" to use dosage instead of hardcalls
2.7 years ago by nhaus ▴ 420
0
votes
1
reply
1.0k
views
What to do if covariates in design matrix of limma are confounded
gene expression differential limma
updated 2.8 years ago by 85k • written 2.8 years ago by ▴ 420
2
votes
2
replies
1.6k
views
Finemapping - how to define a locus?
finemapping locus
updated 2.8 years ago by • 0 • written 3.3 years ago by ▴ 420
2
votes
1
reply
1.1k
views
Comment: Comment: differential expression RNASeq DESeq2
2.8 years ago by nhaus ▴ 420
3
votes
1
reply
1.1k
views
Answer: Answer: differential expression RNASeq DESeq2
2.8 years ago by nhaus ▴ 420
0
votes
0
replies
346
views
Relate longitudinal measurement of quantitative variable with gene expression data
RNA-seq longitudinal
2.8 years ago by nhaus ▴ 420
0
votes
1
reply
577
views
Expression of genes in KEGG pathway
KEGG over representation analysis
updated 2.8 years ago by 11k • written 2.8 years ago by ▴ 420
0
votes
0
replies
420
views
Tools to visualize 2D RNA Heterodimer
visualization RNA
2.8 years ago by nhaus ▴ 420
0
votes
0
replies
3.8k
views
Answer: Answer: Can anyone share me a good GATK4 workflow
3.1 years ago by nhaus ▴ 420
0
votes
0
replies
749
views
Tool: Genotype Imputation Workflow
gwas imputation.
3.2 years ago by nhaus ▴ 420
0
votes
1
reply
1.6k
views
Comment: Comment: Strange speed up in GATK LeftAlignIndels
3.2 years ago by nhaus ▴ 420
15
votes
2
replies
2.3k
views
Tutorial: Germline variant calling pipeline using Snakemake
snakemake GATK germline_variant_calling
updated 2.1 years ago by ▴ 830 • written 3.2 years ago by ▴ 420
2
votes
1
reply
922
views
command line VEP and VEP web interface return different results.
ensembl vep
updated 3.3 years ago by 24k • written 3.3 years ago by ▴ 420
0
votes
0
replies
585
views
Plink genomic inflation estimate
plink inflation genomic GWAS
3.4 years ago by nhaus ▴ 420
1
vote
3
replies
2.5k
views
plink2 tell "--glm" to use dosage instead of hardcalls
plink2 gwas imputation
2.7 years ago by nhaus ▴ 420
1
vote
1
reply
2.5k
views
Answer: Answer: plink2 tell "--glm" to use dosage instead of hardcalls
3.4 years ago by nhaus ▴ 420
0
votes
0
replies
1.6k
views
Minimac4 how is R2 calculated
GWAS minimac4 imputation
3.4 years ago by nhaus ▴ 420
0
votes
0
replies
1.4k
views
Comment: Comment: IMPUTE2 minimal number of SNPs per chunk
3.4 years ago by nhaus ▴ 420
0
votes
2
replies
1.4k
views
Comment: Comment: IMPUTE2 minimal number of SNPs per chunk
3.4 years ago by nhaus ▴ 420
111 results • Page 1 of 3
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