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7
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153
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Tutorial: removeBatchEffect explained using base R linear models
limma effects batch removebatcheffects
updated 2 days ago by 14k • written 2 days ago by ▴ 360
0
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0
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411
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Comment: Comment: differential gene expression analysis when not all samples have an untreated cou
21 days ago by nhaus ▴ 360
2
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2
replies
411
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differential gene expression analysis when not all samples have an untreated counterpart
differential-expression edgeR
21 days ago by nhaus ▴ 360
0
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0
replies
115
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Surrogate variable analysis for paired RNA seq experiment
sva rnaseq ruvseq
28 days ago by nhaus ▴ 360
1
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1
reply
317
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Answer: Answer: Analyzing dataset with counts and TMM values?
11 weeks ago by nhaus ▴ 360
0
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0
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323
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Comment: Comment: pseudobulk differential expression design matrix
11 weeks ago by nhaus ▴ 360
0
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0
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323
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Comment: Comment: pseudobulk differential expression design matrix
11 weeks ago by nhaus ▴ 360
0
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3
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323
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pseudobulk differential expression design matrix
pseudobulk single-cell scRNA-seq
11 weeks ago by nhaus ▴ 360
0
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0
replies
277
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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 ▴ 360
0
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1
reply
613
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GSA type of input data
vst GSEA DESeq2
updated 16 months ago by ★ 7.1k • written 16 months ago by ▴ 360
0
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1
reply
472
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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 ▴ 360
0
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0
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744
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Answer: Answer: How to replace Gene Symbols with Ensembl ID?
18 months ago by nhaus ▴ 360
1
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0
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381
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Libtype differs for all samples although same library preparation
salmon rnaseq libtype
18 months ago by nhaus ▴ 360
1
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1
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2.9k
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Comment: Comment: DESeq2 design formula considerations
18 months ago by nhaus ▴ 360
6
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6
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2.9k
views
DESeq2 design formula considerations
differential RNAseq expression analysis DGE DESeq2
updated 18 months ago by 4.2k • written 18 months ago by ▴ 360
1
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1
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853
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Comment: Comment: gvcf to bam or fastq
19 months ago by nhaus ▴ 360
0
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0
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1.7k
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Comment: Comment: Tuning seurat integration strength to prevent overcorrection
19 months ago by nhaus ▴ 360
0
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1
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1.7k
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Comment: Comment: Tuning seurat integration strength to prevent overcorrection
19 months ago by nhaus ▴ 360
0
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4
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1.7k
views
Tuning seurat integration strength to prevent overcorrection
scRNA seurat
19 months ago by nhaus ▴ 360
2
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1
reply
578
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Answer: Answer: fasta file parsing
20 months ago by nhaus ▴ 360
0
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3
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880
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
0
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0
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880
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Comment: Comment: Function/Package which shows how cells correspond to one another between UMAPs
21 months ago by nhaus ▴ 360
3
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2
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720
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Why do highly expressed genes vary more than lowly expressed genes?
single cell statistics
updated 13 months ago by • 0 • written 21 months ago by ▴ 360
0
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0
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1.2k
views
Comment: Comment: Using Leiden algorithm to cluster bulk RNA samples
2.1 years ago by nhaus ▴ 360
4
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2
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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
505
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 ▴ 360
1
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1
reply
917
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Answer: Answer: Equipment for bioinformatics.
2.1 years ago by nhaus ▴ 360
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
2.2 years ago by nhaus ▴ 360
0
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1
reply
909
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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
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2
replies
1.4k
views
Finemapping - how to define a locus?
finemapping locus
updated 2.2 years ago by • 0 • written 2.8 years ago by ▴ 360
2
votes
1
reply
967
views
Comment: Comment: differential expression RNASeq DESeq2
2.3 years ago by nhaus ▴ 360
3
votes
1
reply
967
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Answer: Answer: differential expression RNASeq DESeq2
2.3 years ago by nhaus ▴ 360
0
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0
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304
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Relate longitudinal measurement of quantitative variable with gene expression data
RNA-seq longitudinal
2.3 years ago by nhaus ▴ 360
0
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1
reply
508
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
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0
replies
364
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Tools to visualize 2D RNA Heterodimer
visualization RNA
2.3 years ago by nhaus ▴ 360
0
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0
replies
3.2k
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Answer: Answer: Can anyone share me a good GATK4 workflow
2.5 years ago by nhaus ▴ 360
0
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0
replies
680
views
Tool: Genotype Imputation Workflow
gwas imputation.
2.6 years ago by nhaus ▴ 360
0
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1
reply
1.4k
views
Comment: Comment: Strange speed up in GATK LeftAlignIndels
2.6 years ago by nhaus ▴ 360
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 19 months ago by ▴ 830 • written 2.6 years ago by ▴ 360
2
votes
1
reply
817
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
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0
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520
views
Plink genomic inflation estimate
plink inflation genomic GWAS
2.8 years ago by nhaus ▴ 360
1
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3
replies
2.1k
views
plink2 tell "--glm" to use dosage instead of hardcalls
plink2 gwas imputation
2.2 years ago by nhaus ▴ 360
1
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1
reply
2.1k
views
Answer: Answer: plink2 tell "--glm" to use dosage instead of hardcalls
2.8 years ago by nhaus ▴ 360
0
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0
replies
1.4k
views
Minimac4 how is R2 calculated
GWAS minimac4 imputation
2.8 years ago by nhaus ▴ 360
0
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0
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1.2k
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Comment: Comment: IMPUTE2 minimal number of SNPs per chunk
2.9 years ago by nhaus ▴ 360
0
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2
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1.2k
views
Comment: Comment: IMPUTE2 minimal number of SNPs per chunk
2.9 years ago by nhaus ▴ 360
2
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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
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1
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618
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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
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0
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617
views
maxT permutation in plink
plink gwas
2.9 years ago by nhaus ▴ 360
0
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0
replies
863
views
Comment: Comment: Why are there nucleotides in the reference genome which are also minor alleles i
2.9 years ago by nhaus ▴ 360
107 results • Page 1 of 3
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