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Showing :
questions
2
votes
2
replies
367
views
differential gene expression analysis when not all samples have an untreated counterpart
differential-expression
edgeR
5 days ago by
nhaus
▴ 300
0
votes
0
replies
103
views
Surrogate variable analysis for paired RNA seq experiment
sva
rnaseq
ruvseq
13 days ago by
nhaus
▴ 300
0
votes
3
replies
283
views
pseudobulk differential expression design matrix
pseudobulk
single-cell
scRNA-seq
9 weeks ago by
nhaus
▴ 300
0
votes
0
replies
272
views
Correcting for covariates in GWAS studies and differential gene expression analysis
batch-correction
GWAS
updated 6 months ago by
Ram
43k • written 6 months ago by
nhaus
▴ 300
0
votes
1
reply
605
views
GSA type of input data
vst
GSEA
DESeq2
updated 16 months ago by
Gordon Smyth
★ 7.0k • written 16 months ago by
nhaus
▴ 300
0
votes
1
reply
461
views
Quantifying GFP and GAL4 reads in drosophila
salmon
qunatification
read
updated 17 months ago by
seidel
11k • written 17 months ago by
nhaus
▴ 300
1
vote
0
replies
378
views
Libtype differs for all samples although same library preparation
salmon
rnaseq
libtype
18 months ago by
nhaus
▴ 300
6
votes
6
replies
2.8k
views
DESeq2 design formula considerations
differential
RNAseq
expression
analysis
DGE
DESeq2
updated 18 months ago by
LauferVA
4.2k • written 18 months ago by
nhaus
▴ 300
0
votes
4
replies
1.6k
views
Tuning seurat integration strength to prevent overcorrection
scRNA
seurat
19 months ago by
nhaus
▴ 300
0
votes
3
replies
868
views
Function/Package which shows how cells correspond to one another between UMAPs
scRNAseq
visualization
updated 21 months ago by
ATpoint
82k • written 21 months ago by
nhaus
▴ 300
3
votes
2
replies
702
views
Why do highly expressed genes vary more than lowly expressed genes?
single
cell
statistics
updated 12 months ago by
Mae
• 0 • written 21 months ago by
nhaus
▴ 300
4
votes
2
replies
1.1k
views
Using Leiden algorithm to cluster bulk RNA samples
clustering
RNAseq
Leiden
2.1 years ago by
nhaus
▴ 300
2
votes
1
reply
496
views
How to check if a certain phenotype is over-represented in a cluster
cluster
overrepresentation
updated 2.1 years ago by
Jean-Karim Heriche
27k • written 2.1 years ago by
nhaus
▴ 300
0
votes
1
reply
887
views
What to do if covariates in design matrix of limma are confounded
gene
expression
differential
limma
updated 2.2 years ago by
ATpoint
82k • written 2.2 years ago by
nhaus
▴ 300
2
votes
2
replies
1.3k
views
Finemapping - how to define a locus?
finemapping
locus
updated 2.2 years ago by
1311703846
• 0 • written 2.8 years ago by
nhaus
▴ 300
0
votes
0
replies
300
views
Relate longitudinal measurement of quantitative variable with gene expression data
RNA-seq
longitudinal
2.2 years ago by
nhaus
▴ 300
0
votes
1
reply
501
views
Expression of genes in KEGG pathway
KEGG
over
representation
analysis
updated 2.2 years ago by
seidel
11k • written 2.2 years ago by
nhaus
▴ 300
0
votes
0
replies
360
views
Tools to visualize 2D RNA Heterodimer
visualization
RNA
2.2 years ago by
nhaus
▴ 300
2
votes
1
reply
807
views
command line VEP and VEP web interface return different results.
ensembl
vep
updated 2.8 years ago by
Emily
23k • written 2.8 years ago by
nhaus
▴ 300
0
votes
0
replies
513
views
Plink genomic inflation estimate
plink
inflation
genomic
GWAS
2.8 years ago by
nhaus
▴ 300
1
vote
3
replies
2.1k
views
plink2 tell "--glm" to use dosage instead of hardcalls
plink2
gwas
imputation
2.1 years ago by
nhaus
▴ 300
0
votes
0
replies
1.4k
views
Minimac4 how is R2 calculated
GWAS
minimac4
imputation
2.8 years ago by
nhaus
▴ 300
2
votes
6
replies
1.2k
views
IMPUTE2 minimal number of SNPs per chunk
impute
gwas
updated 2.8 years ago by
LauferVA
4.2k • written 2.8 years ago by
nhaus
▴ 300
0
votes
1
reply
610
views
IMPUTE2 limit to only one population of 1000G Reference
GWAS
impute
1000g
updated 2.8 years ago by
LauferVA
4.2k • written 2.8 years ago by
nhaus
▴ 300
0
votes
0
replies
609
views
maxT permutation in plink
plink
gwas
2.8 years ago by
nhaus
▴ 300
2
votes
4
replies
854
views
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
WouterDeCoster
47k • written 2.8 years ago by
nhaus
▴ 300
1
vote
1
reply
1.1k
views
What happens to the genotype field in a g.vcf after CombineGVCFs
GT
GATK
CombineGVCFs
genotype
updated 2.8 years ago by
damian.loska
▴ 20 • written 3.0 years ago by
nhaus
▴ 300
2
votes
3
replies
1.9k
views
Ambiguous SNPs
SNPs
updated 2.9 years ago by
Emily
23k • written 2.9 years ago by
nhaus
▴ 300
0
votes
0
replies
426
views
Illumina Omni2.5 genotyping get actual genotypes.
genotyping
omni
illumina
2.9 years ago by
nhaus
▴ 300
2
votes
5
replies
1.3k
views
SHAPEIT v4 modify keep QUAL FORMAT and INFO field
shapeit
phasing
haplotype
2.9 years ago by
nhaus
▴ 300
1
vote
3
replies
1.3k
views
GATK ApplyVQSR filtering doesnt work
gatk
variant
calling
germline
2.9 years ago by
nhaus
▴ 300
1
vote
5
replies
1.9k
views
Liftover vcf file from hs37d5 assembly to b37 assembly
vcf
liftover
assembly
updated 2.6 years ago by
DavidStreid
▴ 90 • written 2.9 years ago by
nhaus
▴ 300
5
votes
2
replies
1.2k
views
High confident germline SNP and INDELS for VQSR for reference genome GRCh37
INDEL
SNP
1000g
GRCh37
3.0 years ago by
nhaus
▴ 300
0
votes
1
reply
658
views
Predicting Drug responds from somatic mutations
prediction
somatic
responds
drug
updated 3.0 years ago by
darklings
▴ 570 • written 3.0 years ago by
nhaus
▴ 300
1
vote
4
replies
1.5k
views
Create Mutational signature plot from vcf file.
R
python
mutational
3.0 years ago by
nhaus
▴ 300
3
votes
5
replies
777
views
conceptual question about paired end sequencing
sequencing
illumina
updated 3.1 years ago by
Ram
43k • written 3.1 years ago by
nhaus
▴ 300
4
votes
5
replies
3.3k
views
VEP is very slow. Fork doesnt seem to work
vep
annotation
2.9 years ago by
nhaus
▴ 300
0
votes
1
reply
807
views
Experience with BaseRecalibratorSpark and ApplyBQSRSpark
gatk
somatic
mutations
snp
updated 3.2 years ago by
colindaven
6.4k • written 3.2 years ago by
nhaus
▴ 300
0
votes
0
replies
873
views
Panel of normals for Mutect2 GRCh37
gatk
broad
mutect2
3.2 years ago by
nhaus
▴ 300
0
votes
5
replies
861
views
biomaRt external_gene_name same entry multiple times when mapping to homolog mouse gene
ensembl
mapping
homology
3.2 years ago by
nhaus
▴ 300
0
votes
0
replies
420
views
chi-square test to identify significantly mutated genes
genome
sequencing
3.2 years ago by
nhaus
▴ 300
0
votes
4
replies
1.3k
views
Duplicated genes in overrepresentation analysis (ORA)
ORA
GSEA
updated 3.3 years ago by
kelen
▴ 200 • written 3.3 years ago by
nhaus
▴ 300
0
votes
0
replies
441
views
Proper way of comparing list of mutated genes
gene
GSEA
3.3 years ago by
nhaus
▴ 300
3
votes
3
replies
982
views
Count, LT, PH, PT Column in Functional Annotation Chart of DAVID
DAVID
GSEA
updated 3.3 years ago by
Asaf
10k • written 3.3 years ago by
nhaus
▴ 300
0
votes
0
replies
638
views
versioned transcripts with SnpEff GRCh37
SnpEff
annotation
3.3 years ago by
nhaus
▴ 300
2
votes
2
replies
868
views
GT 0/0 in VCF file
genome
3.4 years ago by
nhaus
▴ 300
0
votes
3
replies
631
views
Using StringTie with CAGE-seq data
StringTie
3.7 years ago by
nhaus
▴ 300
0
votes
5
replies
2.6k
views
Merging BAM vs concatenate FASTQ
sequencing
genome
3.7 years ago by
nhaus
▴ 300
4
votes
9
replies
2.8k
views
Questions about reference genome and alignment
genome
alignment
assembly
updated 3.7 years ago by
JC
13k • written 3.7 years ago by
nhaus
▴ 300
1
vote
1
reply
911
views
How to download BAM file from VM
bam
VM
updated 13 months ago by
Ram
43k • written 3.8 years ago by
nhaus
▴ 300
57 results • Page
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