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1
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5
replies
2.4k
views
Shannon vs Simpson for TCR diversity estimation
TCR shannon simpson
updated 28 days ago by 82k • written 5.1 years ago by ▴ 750
0
votes
1
reply
185
views
How to reveal real AF of variant if duplicates can't be removed (such as in amplicon-seq)
allele-frequency amplicon-seq
updated 28 days ago by 43k • written 29 days ago by ▴ 750
2
votes
5
replies
3.9k
views
Any tools for predicting binding affinity between TCR and epitode?
prediction TCR cancer
updated 3 months ago by • 0 • written 5.9 years ago by ▴ 750
2
votes
3
replies
984
views
Method to detect genome doubling
CNV genome doubling
updated 17 days ago by 4.2k • written 4.5 years ago by ▴ 750
2
votes
6
replies
1.7k
views
Can we get absolute abundance of TCR using TCR-Seq?
TCR-Seq
updated 15 months ago by ▴ 60 • written 5.4 years ago by ▴ 750
0
votes
1
reply
1.6k
views
Wilcoxon test, t-test and negative binomial test for DEG of scRNA-Seq data
scRNA-Seq DEG differential expression
updated 18 months ago by 13k • written 3.6 years ago by ▴ 750
0
votes
0
replies
677
views
Why case-controlled study is more bias prone than cohort study?
case-controlled study cohort study confounder
written 3.5 years ago by ▴ 750
0
votes
0
replies
329
views
Which distribution to choose for ploting mutant allele frequency?
distribution SNV
19 months ago by CY ▴ 750
0
votes
1
reply
508
views
Reference material for distinguishing focal CNV and chromosome CNV
CNV
updated 2.3 years ago by ★ 2.9k • written 2.3 years ago by ▴ 750
0
votes
1
reply
883
views
What is the well-recognized standard of coverage uniformity
sequencing CNV depth uniformity coverage
updated 2.8 years ago by ★ 2.9k • written 2.8 years ago by ▴ 750
0
votes
1
reply
720
views
Detection of biallelic mutation (inactivation)
somatic biallelic mutation
updated 2.9 years ago by ▴ 160 • written 2.9 years ago by ▴ 750
0
votes
2
replies
619
views
Violation of Independence test for differential methylation (DM)
methylation differential methylation
3.2 years ago by CY ▴ 750
3
votes
3
replies
1.3k
views
Treat methylation as binary or continuous signal when detecting DMR?
methylation
3.6 years ago by CY ▴ 750
5
votes
1
reply
1.2k
views
Is definition of differentially methylated region (DMR) biologically meaningful?
methylation DMR
updated 3.7 years ago by 3.2k • written 3.7 years ago by ▴ 750
0
votes
2
replies
1.1k
views
Defining methylation level of CpG island
methylation CpG island
3.7 years ago by CY ▴ 750
0
votes
3
replies
851
views
How to derive sequence of novel transcript identified by Cufflinks
transcript RNA-Seq
3.7 years ago by CY ▴ 750
0
votes
0
replies
493
views
Did and why recent studies show superior predictive power using methylation data on early cancer detection
methylation cancer detection
3.8 years ago by CY ▴ 750
0
votes
0
replies
669
views
Example code of MCMC on somatic variant calling (site specific error model)
Variant calling
3.9 years ago by CY ▴ 750
0
votes
0
replies
475
views
Create synthetic data based on general description of molecular characteristic for modeling
next-gen
4.0 years ago by CY ▴ 750
13
votes
9
replies
3.7k
views
Why NB distribution is preferred in RNA-Seq while normal distribution is preferred in microarray?
RNA-Seq Microarray
updated 24 months ago by ★ 6.0k • written 4.0 years ago by ▴ 750
0
votes
2
replies
999
views
Logit-normal distribution to model variation among biological replicates
rMATS alternative splicing distribution
updated 4.1 years ago by 87k • written 4.1 years ago by ▴ 750
0
votes
1
reply
780
views
How does aligner determine strandness when doing alignment
alignment
4.2 years ago by CY ▴ 750
0
votes
4
replies
1.1k
views
Would curated pathway gene set better being weighted than being binary
RNA-Seq enrichment analysis
updated 4.2 years ago by 20 • written 4.3 years ago by ▴ 750
0
votes
3
replies
879
views
Distinguishing real RNA-editing event from sequencing artifact due to reverse transcription
RNA-editing sequencing artifact
4.2 years ago by CY ▴ 750
1
vote
2
replies
1.1k
views
Detection of CNV(InDel) of intermediate size
CNV InDel
2.9 years ago by CY ▴ 750
2
votes
3
replies
993
views
Identifying zygosity of somatic deletion
CNV
updated 4.2 years ago by ▴ 460 • written 4.2 years ago by ▴ 750
0
votes
3
replies
1.0k
views
In PCA on RNA-Seq data, what does Gaussian distribution refer to?
RNA-Seq PCA Gaussian
updated 4.3 years ago by 104k • written 4.3 years ago by ▴ 750
0
votes
2
replies
920
views
Does variant enrichment analysis make sense?
enrichment analysis somatic variant expression
4.4 years ago by CY ▴ 750
6
votes
6
replies
1.3k
views
Arm-level SCNA does not change mRNA expression level?
CNV SCNA expression
4.4 years ago by CY ▴ 750
2
votes
7
replies
1.3k
views
Why can we still be able to continuously discover new cancer driver bioinformatically these days?
driver gene cancer
4.4 years ago by CY ▴ 750
1
vote
5
replies
1.1k
views
Composition of low mappable region in human genome
mappability repetitive region homologous region
updated 4.5 years ago by 20 • written 4.6 years ago by ▴ 750
0
votes
0
replies
632
views
Any absolute quantification method for detection of polyploidy tumor sample
PCR RNA-Seq
4.6 years ago by CY ▴ 750
1
vote
2
replies
1.2k
views
How splice-aware aligner (RNA-Seq) deal with long gap (intron) penalty
RNA-Seq STAR alignment hisat tophat
updated 4.6 years ago by 20 • written 4.6 years ago by ▴ 750
1
vote
3
replies
888
views
How does base quality / mapping quality affect germline calling
haplotypecaller germline calling MAPQ
4.6 years ago by CY ▴ 750
0
votes
4
replies
1.3k
views
non-reference allele didn't be called into vcf by HC
haplotypecaller vcf
updated 4.6 years ago by 87k • written 4.6 years ago by ▴ 750
0
votes
1
reply
918
views
Dispersion shrinkage in DESeq2: LOESS instead of negative binomial based GLM?
RNA-SEQ DESeq
4.7 years ago by CY ▴ 750
1
vote
5
replies
953
views
Archieve of homologous nucleotide sequence across genome
sequence
updated 4.7 years ago by ▴ 130 • written 4.7 years ago by ▴ 750
0
votes
0
replies
980
views
XHMM calls CNV on a number of normal samples
CNV XHH
4.7 years ago by CY ▴ 750
0
votes
9
replies
1.6k
views
Library size normalization during CNV calling from genomically doubled tumor tissue
CNV
updated 4.7 years ago by ▴ 550 • written 4.7 years ago by ▴ 750
6
votes
5
replies
1.3k
views
Noisy CNV background in old FFPE sample
CNV FFPE
updated 4.8 years ago by ★ 2.8k • written 4.8 years ago by ▴ 750
1
vote
3
replies
966
views
Effect size in power analysis when dealing with Poisson based variant caller
variant calling
updated 4.8 years ago by ▴ 550 • written 4.8 years ago by ▴ 750
0
votes
0
replies
1.1k
views
Difference between mpileup and HaplotypeCaller -ERC BP_RESOLUTION
variant calling haplotypecaller mpileup
4.8 years ago by CY ▴ 750
3
votes
7
replies
1.4k
views
Why methylation sequencing requires much less sequencing depth than DNA-Seq?
methylation WGBS
updated 4.9 years ago by 8.2k • written 4.9 years ago by ▴ 750
21
votes
4
replies
1.6k
views
Why do so many biomarker based classifiers claim high accuracy but rarely used in clinical setting?
biomarker
4.9 years ago by CY ▴ 750
0
votes
1
reply
949
views
Mutated gene based pathway enrichment
enrichment mutation
updated 4.9 years ago by ▴ 990 • written 4.9 years ago by ▴ 750
0
votes
0
replies
794
views
Why seed and fuzzy-search in MIGEC?
MIGEC MUI tcr
5.0 years ago by CY ▴ 750
27
votes
17
replies
9.6k
views
Why can't use t-test for differential expression (negative binomial distribution assumed)
RNA-Seq
updated 5.0 years ago by 14k • written 5.0 years ago by ▴ 750
2
votes
12
replies
2.1k
views
Multiple testing correction issue
multiple testing correction
updated 5.1 years ago by 14k • written 5.1 years ago by ▴ 750
0
votes
1
reply
1.2k
views
Tools that make mutation based phylogenetic tree figure
phylogenetic heterogeneity
5.1 years ago by CY ▴ 750
0
votes
0
replies
827
views
intuitive explaination of using HMM for alignment
HMM alignment
5.1 years ago by CY ▴ 750
117 results • Page 1 of 3
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