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0
votes
4
replies
553
views
Is there a common acceptance criteria for sample contamination?
contamination
updated 4 months ago by ★ 17k • written 4 months ago by ▴ 750
1
vote
5
replies
2.7k
views
Shannon vs Simpson for TCR diversity estimation
TCR shannon simpson
updated 5 months ago by 84k • written 5.5 years ago by ▴ 750
0
votes
1
reply
274
views
How to reveal real AF of variant if duplicates can't be removed (such as in amplicon-seq)
allele-frequency amplicon-seq
updated 5 months ago by 44k • written 5 months ago by ▴ 750
2
votes
5
replies
4.1k
views
Any tools for predicting binding affinity between TCR and epitode?
prediction TCR cancer
updated 8 months ago by • 0 • written 6.3 years ago by ▴ 750
2
votes
3
replies
1.1k
views
Method to detect genome doubling
CNV genome doubling
updated 5 months ago by 4.4k • written 4.9 years ago by ▴ 750
2
votes
6
replies
1.9k
views
Can we get absolute abundance of TCR using TCR-Seq?
TCR-Seq
updated 20 months ago by ▴ 60 • written 5.8 years ago by ▴ 750
0
votes
1
reply
1.7k
views
Wilcoxon test, t-test and negative binomial test for DEG of scRNA-Seq data
scRNA-Seq DEG differential expression
updated 23 months ago by 13k • written 4.0 years ago by ▴ 750
0
votes
0
replies
720
views
Why case-controlled study is more bias prone than cohort study?
case-controlled study cohort study confounder
written 3.9 years ago by ▴ 750
0
votes
0
replies
386
views
Which distribution to choose for ploting mutant allele frequency?
distribution SNV
23 months ago by CY ▴ 750
0
votes
1
reply
581
views
Reference material for distinguishing focal CNV and chromosome CNV
CNV
updated 2.8 years ago by ★ 2.9k • written 2.8 years ago by ▴ 750
0
votes
1
reply
968
views
What is the well-recognized standard of coverage uniformity
sequencing CNV depth uniformity coverage
updated 3.3 years ago by ★ 2.9k • written 3.3 years ago by ▴ 750
0
votes
1
reply
809
views
Detection of biallelic mutation (inactivation)
somatic biallelic mutation
updated 3.3 years ago by ▴ 160 • written 3.3 years ago by ▴ 750
0
votes
2
replies
687
views
Violation of Independence test for differential methylation (DM)
methylation differential methylation
3.6 years ago by CY ▴ 750
3
votes
3
replies
1.4k
views
Treat methylation as binary or continuous signal when detecting DMR?
methylation
4.1 years ago by CY ▴ 750
5
votes
1
reply
1.3k
views
Is definition of differentially methylated region (DMR) biologically meaningful?
methylation DMR
updated 4.1 years ago by 3.2k • written 4.1 years ago by ▴ 750
0
votes
2
replies
1.2k
views
Defining methylation level of CpG island
methylation CpG island
4.1 years ago by CY ▴ 750
0
votes
3
replies
946
views
How to derive sequence of novel transcript identified by Cufflinks
transcript RNA-Seq
4.1 years ago by CY ▴ 750
0
votes
0
replies
529
views
Did and why recent studies show superior predictive power using methylation data on early cancer detection
methylation cancer detection
4.3 years ago by CY ▴ 750
0
votes
0
replies
709
views
Example code of MCMC on somatic variant calling (site specific error model)
Variant calling
4.3 years ago by CY ▴ 750
0
votes
0
replies
509
views
Create synthetic data based on general description of molecular characteristic for modeling
next-gen
4.4 years ago by CY ▴ 750
13
votes
9
replies
4.0k
views
Why NB distribution is preferred in RNA-Seq while normal distribution is preferred in microarray?
RNA-Seq Microarray
updated 2.4 years ago by ★ 6.9k • written 4.4 years ago by ▴ 750
0
votes
2
replies
1.1k
views
Logit-normal distribution to model variation among biological replicates
rMATS alternative splicing distribution
updated 4.5 years ago by 88k • written 4.5 years ago by ▴ 750
0
votes
1
reply
839
views
How does aligner determine strandness when doing alignment
alignment
4.6 years ago by CY ▴ 750
0
votes
4
replies
1.2k
views
Would curated pathway gene set better being weighted than being binary
RNA-Seq enrichment analysis
updated 4.6 years ago by 20 • written 4.7 years ago by ▴ 750
0
votes
3
replies
998
views
Distinguishing real RNA-editing event from sequencing artifact due to reverse transcription
RNA-editing sequencing artifact
4.6 years ago by CY ▴ 750
1
vote
2
replies
1.2k
views
Detection of CNV(InDel) of intermediate size
CNV InDel
3.3 years ago by CY ▴ 750
2
votes
3
replies
1.1k
views
Identifying zygosity of somatic deletion
CNV
updated 4.6 years ago by ▴ 470 • written 4.6 years ago by ▴ 750
0
votes
3
replies
1.1k
views
In PCA on RNA-Seq data, what does Gaussian distribution refer to?
RNA-Seq PCA Gaussian
updated 4.7 years ago by 104k • written 4.7 years ago by ▴ 750
0
votes
2
replies
1.0k
views
Does variant enrichment analysis make sense?
enrichment analysis somatic variant expression
4.9 years ago by CY ▴ 750
6
votes
6
replies
1.5k
views
Arm-level SCNA does not change mRNA expression level?
CNV SCNA expression
4.9 years ago by CY ▴ 750
2
votes
7
replies
1.4k
views
Why can we still be able to continuously discover new cancer driver bioinformatically these days?
driver gene cancer
4.9 years ago by CY ▴ 750
1
vote
5
replies
1.2k
views
Composition of low mappable region in human genome
mappability repetitive region homologous region
updated 5.0 years ago by 20 • written 5.0 years ago by ▴ 750
0
votes
0
replies
664
views
Any absolute quantification method for detection of polyploidy tumor sample
PCR RNA-Seq
5.0 years ago by CY ▴ 750
1
vote
2
replies
1.3k
views
How splice-aware aligner (RNA-Seq) deal with long gap (intron) penalty
RNA-Seq STAR alignment hisat tophat
updated 5.0 years ago by 20 • written 5.0 years ago by ▴ 750
1
vote
3
replies
995
views
How does base quality / mapping quality affect germline calling
haplotypecaller germline calling MAPQ
5.0 years ago by CY ▴ 750
0
votes
4
replies
1.4k
views
non-reference allele didn't be called into vcf by HC
haplotypecaller vcf
updated 5.0 years ago by 88k • written 5.0 years ago by ▴ 750
0
votes
1
reply
1000
views
Dispersion shrinkage in DESeq2: LOESS instead of negative binomial based GLM?
RNA-SEQ DESeq
5.1 years ago by CY ▴ 750
1
vote
5
replies
1.1k
views
Archieve of homologous nucleotide sequence across genome
sequence
updated 5.1 years ago by ▴ 130 • written 5.1 years ago by ▴ 750
0
votes
0
replies
1.0k
views
XHMM calls CNV on a number of normal samples
CNV XHH
5.1 years ago by CY ▴ 750
0
votes
9
replies
1.8k
views
Library size normalization during CNV calling from genomically doubled tumor tissue
CNV
updated 5.2 years ago by ▴ 550 • written 5.2 years ago by ▴ 750
6
votes
5
replies
1.4k
views
Noisy CNV background in old FFPE sample
CNV FFPE
updated 5.2 years ago by ★ 2.8k • written 5.2 years ago by ▴ 750
1
vote
3
replies
1.1k
views
Effect size in power analysis when dealing with Poisson based variant caller
variant calling
updated 5.2 years ago by ▴ 550 • written 5.2 years ago by ▴ 750
0
votes
0
replies
1.1k
views
Difference between mpileup and HaplotypeCaller -ERC BP_RESOLUTION
variant calling haplotypecaller mpileup
5.2 years ago by CY ▴ 750
3
votes
7
replies
1.7k
views
Why methylation sequencing requires much less sequencing depth than DNA-Seq?
methylation WGBS
updated 5.3 years ago by 8.3k • written 5.3 years ago by ▴ 750
21
votes
4
replies
1.7k
views
Why do so many biomarker based classifiers claim high accuracy but rarely used in clinical setting?
biomarker
5.3 years ago by CY ▴ 750
0
votes
1
reply
1.0k
views
Mutated gene based pathway enrichment
enrichment mutation
updated 5.3 years ago by ▴ 990 • written 5.3 years ago by ▴ 750
0
votes
0
replies
850
views
Why seed and fuzzy-search in MIGEC?
MIGEC MUI tcr
5.4 years ago by CY ▴ 750
27
votes
17
replies
10k
views
Why can't use t-test for differential expression (negative binomial distribution assumed)
RNA-Seq
updated 5.5 years ago by 14k • written 5.5 years ago by ▴ 750
2
votes
12
replies
2.4k
views
Multiple testing correction issue
multiple testing correction
updated 5.5 years ago by 14k • written 5.5 years ago by ▴ 750
0
votes
1
reply
1.3k
views
Tools that make mutation based phylogenetic tree figure
phylogenetic heterogeneity
5.5 years ago by CY ▴ 750
118 results • Page 1 of 3
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