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12
votes
5
replies
2.8k
views
Tutorial: removeBatchEffect explained using base R linear models
removebatcheffects limma batch-effect
updated 10 months ago by ▴ 150 • written 16 months ago by ▴ 420
0
votes
1
reply
1.1k
views
Using Pseudobulk Approach for Identifying Marker Genes Within a Single Condition
differential-expression single-cell pseudobulk
updated 14 months ago by 89k • written 14 months ago by ▴ 420
0
votes
0
replies
479
views
Linear Mixed Model for Differential Gene Expression in Single-Cell RNAseq with Batch Effects
MAST differential-expression lmer
updated 14 months ago by 45k • written 14 months ago by ▴ 420
0
votes
0
replies
769
views
Comment: Comment: Specifying a variable as a random effect in model.matrix()
14 months ago by nhaus ▴ 420
1
vote
2
replies
851
views
Go from protein mutation back to gene mutation
mutations tools
updated 15 months ago by 153k • written 16 months ago by ▴ 420
0
votes
0
replies
1.1k
views
Comment: Comment: differential gene expression analysis when not all samples have an untreated cou
17 months ago by nhaus ▴ 420
2
votes
2
replies
1.1k
views
differential gene expression analysis when not all samples have an untreated counterpart
differential-expression edgeR
17 months ago by nhaus ▴ 420
0
votes
0
replies
455
views
Surrogate variable analysis for paired RNA seq experiment
sva rnaseq ruvseq
17 months ago by nhaus ▴ 420
1
vote
1
reply
864
views
Answer: Answer: Analyzing dataset with counts and TMM values?
19 months ago by nhaus ▴ 420
0
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0
replies
1.0k
views
Comment: Comment: pseudobulk differential expression design matrix
19 months ago by nhaus ▴ 420
0
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0
replies
1.0k
views
Comment: Comment: pseudobulk differential expression design matrix
19 months ago by nhaus ▴ 420
0
votes
3
replies
1.0k
views
pseudobulk differential expression design matrix
pseudobulk single-cell scRNA-seq
19 months ago by nhaus ▴ 420
0
votes
0
replies
581
views
Correcting for covariates in GWAS studies and differential gene expression analysis
batch-correction GWAS
updated 23 months ago by 45k • written 23 months ago by ▴ 420
0
votes
1
reply
1.0k
views
GSA type of input data
vst GSEA DESeq2
updated 2.7 years ago by ★ 8.3k • written 2.7 years ago by ▴ 420
0
votes
1
reply
830
views
Quantifying GFP and GAL4 reads in drosophila
salmon qunatification read
updated 2.9 years ago by 11k • written 2.9 years ago by ▴ 420
0
votes
0
replies
1.2k
views
Answer: Answer: How to replace Gene Symbols with Ensembl ID?
2.9 years ago by nhaus ▴ 420
1
vote
0
replies
633
views
Libtype differs for all samples although same library preparation
salmon rnaseq libtype
2.9 years ago by nhaus ▴ 420
1
vote
1
reply
6.2k
views
Comment: Comment: DESeq2 design formula considerations
2.9 years ago by nhaus ▴ 420
7
votes
6
replies
6.2k
views
DESeq2 design formula considerations
differential RNAseq expression analysis DGE DESeq2
updated 2.9 years ago by 4.8k • written 2.9 years ago by ▴ 420
1
vote
1
reply
1.5k
views
Comment: Comment: gvcf to bam or fastq
3.0 years ago by nhaus ▴ 420
0
votes
0
replies
3.2k
views
Comment: Comment: Tuning seurat integration strength to prevent overcorrection
3.0 years ago by nhaus ▴ 420
0
votes
1
reply
3.2k
views
Comment: Comment: Tuning seurat integration strength to prevent overcorrection
3.0 years ago by nhaus ▴ 420
0
votes
4
replies
3.2k
views
Tuning seurat integration strength to prevent overcorrection
scRNA seurat
3.0 years ago by nhaus ▴ 420
2
votes
1
reply
997
views
Answer: Answer: fasta file parsing
3.1 years ago by nhaus ▴ 420
0
votes
3
replies
1.3k
views
Function/Package which shows how cells correspond to one another between UMAPs
scRNAseq visualization
updated 3.2 years ago by 89k • written 3.2 years ago by ▴ 420
0
votes
0
replies
1.3k
views
Comment: Comment: Function/Package which shows how cells correspond to one another between UMAPs
3.2 years ago by nhaus ▴ 420
3
votes
2
replies
1.2k
views
Why do highly expressed genes vary more than lowly expressed genes?
single cell statistics
updated 2.5 years ago by • 0 • written 3.2 years ago by ▴ 420
0
votes
0
replies
2.5k
views
Comment: Comment: Using Leiden algorithm to cluster bulk RNA samples
3.5 years ago by nhaus ▴ 420
4
votes
2
replies
2.5k
views
Using Leiden algorithm to cluster bulk RNA samples
clustering RNAseq Leiden
3.5 years ago by nhaus ▴ 420
2
votes
1
reply
965
views
How to check if a certain phenotype is over-represented in a cluster
cluster overrepresentation
updated 3.5 years ago by 27k • written 3.5 years ago by ▴ 420
1
vote
1
reply
1.5k
views
Answer: Answer: Equipment for bioinformatics.
3.5 years ago by nhaus ▴ 420
0
votes
0
replies
3.4k
views
Comment: Comment: plink2 tell "--glm" to use dosage instead of hardcalls
3.5 years ago by nhaus ▴ 420
0
votes
1
reply
1.3k
views
What to do if covariates in design matrix of limma are confounded
gene expression differential limma
updated 3.6 years ago by 89k • written 3.6 years ago by ▴ 420
2
votes
2
replies
2.2k
views
Finemapping - how to define a locus?
finemapping locus
updated 3.6 years ago by • 0 • written 4.2 years ago by ▴ 420
2
votes
1
reply
1.5k
views
Comment: Comment: differential expression RNASeq DESeq2
3.6 years ago by nhaus ▴ 420
3
votes
1
reply
1.5k
views
Answer: Answer: differential expression RNASeq DESeq2
3.6 years ago by nhaus ▴ 420
0
votes
0
replies
501
views
Relate longitudinal measurement of quantitative variable with gene expression data
RNA-seq longitudinal
3.6 years ago by nhaus ▴ 420
0
votes
1
reply
786
views
Expression of genes in KEGG pathway
KEGG over representation analysis
updated 3.7 years ago by 11k • written 3.7 years ago by ▴ 420
0
votes
0
replies
607
views
Tools to visualize 2D RNA Heterodimer
visualization RNA
3.7 years ago by nhaus ▴ 420
0
votes
0
replies
5.1k
views
Answer: Answer: Can anyone share me a good GATK4 workflow
3.9 years ago by nhaus ▴ 420
0
votes
0
replies
948
views
Tool: Genotype Imputation Workflow
gwas imputation.
4.0 years ago by nhaus ▴ 420
0
votes
1
reply
2.3k
views
Comment: Comment: Strange speed up in GATK LeftAlignIndels
4.0 years ago by nhaus ▴ 420
15
votes
2
replies
2.8k
views
Tutorial: Germline variant calling pipeline using Snakemake
snakemake GATK germline_variant_calling
updated 3.0 years ago by ▴ 840 • written 4.0 years ago by ▴ 420
2
votes
1
reply
1.3k
views
command line VEP and VEP web interface return different results.
ensembl vep
updated 4.2 years ago by 24k • written 4.2 years ago by ▴ 420
0
votes
0
replies
802
views
Plink genomic inflation estimate
plink inflation genomic GWAS
4.2 years ago by nhaus ▴ 420
1
vote
3
replies
3.4k
views
plink2 tell "--glm" to use dosage instead of hardcalls
plink2 gwas imputation
3.5 years ago by nhaus ▴ 420
1
vote
1
reply
3.4k
views
Answer: Answer: plink2 tell "--glm" to use dosage instead of hardcalls
4.2 years ago by nhaus ▴ 420
0
votes
0
replies
2.0k
views
Minimac4 how is R2 calculated
GWAS minimac4 imputation
4.2 years ago by nhaus ▴ 420
0
votes
0
replies
2.0k
views
Comment: Comment: IMPUTE2 minimal number of SNPs per chunk
4.2 years ago by nhaus ▴ 420
0
votes
2
replies
2.0k
views
Comment: Comment: IMPUTE2 minimal number of SNPs per chunk
4.2 years ago by nhaus ▴ 420
111 results • Page 1 of 3
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