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12
votes
5
replies
3.2k
views
Tutorial: removeBatchEffect explained using base R linear models
removebatcheffects limma batch-effect
updated 12 months ago by ▴ 150 • written 18 months ago by ▴ 420
0
votes
1
reply
1.3k
views
Using Pseudobulk Approach for Identifying Marker Genes Within a Single Condition
differential-expression single-cell pseudobulk
updated 16 months ago by 90k • written 16 months ago by ▴ 420
0
votes
0
replies
554
views
Linear Mixed Model for Differential Gene Expression in Single-Cell RNAseq with Batch Effects
MAST differential-expression lmer
updated 16 months ago by 45k • written 16 months ago by ▴ 420
0
votes
0
replies
825
views
Comment: Comment: Specifying a variable as a random effect in model.matrix()
16 months ago by nhaus ▴ 420
1
vote
2
replies
914
views
Go from protein mutation back to gene mutation
mutations tools
updated 17 months ago by 154k • written 17 months ago by ▴ 420
0
votes
0
replies
1.2k
views
Comment: Comment: differential gene expression analysis when not all samples have an untreated cou
19 months ago by nhaus ▴ 420
2
votes
2
replies
1.2k
views
differential gene expression analysis when not all samples have an untreated counterpart
differential-expression edgeR
19 months ago by nhaus ▴ 420
0
votes
0
replies
509
views
Surrogate variable analysis for paired RNA seq experiment
sva rnaseq ruvseq
19 months ago by nhaus ▴ 420
1
vote
1
reply
970
views
Answer: Answer: Analyzing dataset with counts and TMM values?
20 months ago by nhaus ▴ 420
0
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0
replies
1.1k
views
Comment: Comment: pseudobulk differential expression design matrix
20 months ago by nhaus ▴ 420
0
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0
replies
1.1k
views
Comment: Comment: pseudobulk differential expression design matrix
20 months ago by nhaus ▴ 420
0
votes
3
replies
1.1k
views
pseudobulk differential expression design matrix
pseudobulk single-cell scRNA-seq
20 months ago by nhaus ▴ 420
0
votes
0
replies
630
views
Correcting for covariates in GWAS studies and differential gene expression analysis
batch-correction GWAS
updated 2.1 years ago by 45k • written 2.1 years ago by ▴ 420
0
votes
1
reply
1.1k
views
GSA type of input data
vst GSEA DESeq2
updated 2.9 years ago by ★ 8.5k • written 2.9 years ago by ▴ 420
0
votes
1
reply
887
views
Quantifying GFP and GAL4 reads in drosophila
salmon qunatification read
updated 3.0 years ago by 11k • written 3.0 years ago by ▴ 420
0
votes
0
replies
1.2k
views
Answer: Answer: How to replace Gene Symbols with Ensembl ID?
3.0 years ago by nhaus ▴ 420
1
vote
0
replies
666
views
Libtype differs for all samples although same library preparation
salmon rnaseq libtype
3.0 years ago by nhaus ▴ 420
1
vote
1
reply
6.8k
views
Comment: Comment: DESeq2 design formula considerations
3.0 years ago by nhaus ▴ 420
7
votes
6
replies
6.8k
views
DESeq2 design formula considerations
differential RNAseq expression analysis DGE DESeq2
updated 3.0 years ago by 4.8k • written 3.0 years ago by ▴ 420
1
vote
1
reply
1.6k
views
Comment: Comment: gvcf to bam or fastq
3.1 years ago by nhaus ▴ 420
0
votes
0
replies
3.5k
views
Comment: Comment: Tuning seurat integration strength to prevent overcorrection
3.1 years ago by nhaus ▴ 420
0
votes
1
reply
3.5k
views
Comment: Comment: Tuning seurat integration strength to prevent overcorrection
3.1 years ago by nhaus ▴ 420
0
votes
4
replies
3.5k
views
Tuning seurat integration strength to prevent overcorrection
scRNA seurat
3.1 years ago by nhaus ▴ 420
2
votes
1
reply
1.1k
views
Answer: Answer: fasta file parsing
3.2 years ago by nhaus ▴ 420
0
votes
3
replies
1.4k
views
Function/Package which shows how cells correspond to one another between UMAPs
scRNAseq visualization
updated 3.3 years ago by 90k • written 3.3 years ago by ▴ 420
0
votes
0
replies
1.4k
views
Comment: Comment: Function/Package which shows how cells correspond to one another between UMAPs
3.3 years ago by nhaus ▴ 420
3
votes
2
replies
1.3k
views
Why do highly expressed genes vary more than lowly expressed genes?
single cell statistics
updated 2.6 years ago by • 0 • written 3.3 years ago by ▴ 420
0
votes
0
replies
2.7k
views
Comment: Comment: Using Leiden algorithm to cluster bulk RNA samples
3.6 years ago by nhaus ▴ 420
4
votes
2
replies
2.7k
views
Using Leiden algorithm to cluster bulk RNA samples
clustering RNAseq Leiden
3.6 years ago by nhaus ▴ 420
2
votes
1
reply
1.0k
views
How to check if a certain phenotype is over-represented in a cluster
cluster overrepresentation
updated 3.6 years ago by 27k • written 3.6 years ago by ▴ 420
1
vote
1
reply
1.6k
views
Answer: Answer: Equipment for bioinformatics.
3.6 years ago by nhaus ▴ 420
0
votes
0
replies
3.7k
views
Comment: Comment: plink2 tell "--glm" to use dosage instead of hardcalls
3.7 years ago by nhaus ▴ 420
0
votes
1
reply
1.4k
views
What to do if covariates in design matrix of limma are confounded
gene expression differential limma
updated 3.7 years ago by 90k • written 3.7 years ago by ▴ 420
2
votes
2
replies
2.3k
views
Finemapping - how to define a locus?
finemapping locus
updated 3.8 years ago by • 0 • written 4.3 years ago by ▴ 420
2
votes
1
reply
1.6k
views
Comment: Comment: differential expression RNASeq DESeq2
3.8 years ago by nhaus ▴ 420
3
votes
1
reply
1.6k
views
Answer: Answer: differential expression RNASeq DESeq2
3.8 years ago by nhaus ▴ 420
0
votes
0
replies
528
views
Relate longitudinal measurement of quantitative variable with gene expression data
RNA-seq longitudinal
3.8 years ago by nhaus ▴ 420
0
votes
1
reply
823
views
Expression of genes in KEGG pathway
KEGG over representation analysis
updated 3.8 years ago by 11k • written 3.8 years ago by ▴ 420
0
votes
0
replies
638
views
Tools to visualize 2D RNA Heterodimer
visualization RNA
3.8 years ago by nhaus ▴ 420
0
votes
0
replies
5.3k
views
Answer: Answer: Can anyone share me a good GATK4 workflow
4.0 years ago by nhaus ▴ 420
0
votes
0
replies
988
views
Tool: Genotype Imputation Workflow
gwas imputation.
4.1 years ago by nhaus ▴ 420
0
votes
1
reply
2.4k
views
Comment: Comment: Strange speed up in GATK LeftAlignIndels
4.1 years ago by nhaus ▴ 420
15
votes
2
replies
2.9k
views
Tutorial: Germline variant calling pipeline using Snakemake
snakemake GATK germline_variant_calling
updated 3.1 years ago by ▴ 840 • written 4.1 years ago by ▴ 420
2
votes
1
reply
1.3k
views
command line VEP and VEP web interface return different results.
ensembl vep
updated 4.3 years ago by 24k • written 4.3 years ago by ▴ 420
0
votes
0
replies
849
views
Plink genomic inflation estimate
plink inflation genomic GWAS
4.3 years ago by nhaus ▴ 420
1
vote
3
replies
3.7k
views
plink2 tell "--glm" to use dosage instead of hardcalls
plink2 gwas imputation
3.7 years ago by nhaus ▴ 420
1
vote
1
reply
3.7k
views
Answer: Answer: plink2 tell "--glm" to use dosage instead of hardcalls
4.3 years ago by nhaus ▴ 420
0
votes
0
replies
2.1k
views
Minimac4 how is R2 calculated
GWAS minimac4 imputation
4.4 years ago by nhaus ▴ 420
0
votes
0
replies
2.2k
views
Comment: Comment: IMPUTE2 minimal number of SNPs per chunk
4.4 years ago by nhaus ▴ 420
0
votes
2
replies
2.2k
views
Comment: Comment: IMPUTE2 minimal number of SNPs per chunk
4.4 years ago by nhaus ▴ 420
111 results • Page 1 of 3
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