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2
votes
6
replies
1.3k
views
Can we get absolute abundance of TCR using TCR-Seq?
TCR-Seq
updated 8 weeks ago by ▴ 60 • written 4.2 years ago by ▴ 710
1
vote
4
replies
1.5k
views
Shannon vs Simpson for TCR diversity estimation
TCR shannon simpson
updated 8 weeks ago by ▴ 60 • written 4.0 years ago by ▴ 710
0
votes
1
reply
1.2k
views
Wilcoxon test, t-test and negative binomial test for DEG of scRNA-Seq data
scRNA-Seq DEG differential expression
updated 5 months ago by 11k • written 2.4 years ago by ▴ 710
0
votes
0
replies
522
views
Why case-controlled study is more bias prone than cohort study?
case-controlled study cohort study confounder
written 2.4 years ago by ▴ 710
0
votes
0
replies
172
views
Which distribution to choose for ploting mutant allele frequency?
distribution SNV
5 months ago by CY ▴ 710
0
votes
1
reply
305
views
Reference material for distinguishing focal CNV and chromosome CNV
CNV
updated 14 months ago by ★ 2.9k • written 14 months ago by ▴ 710
0
votes
1
reply
647
views
What is the well-recognized standard of coverage uniformity
sequencing CNV depth uniformity coverage
updated 20 months ago by ★ 2.9k • written 20 months ago by ▴ 710
0
votes
1
reply
484
views
Detection of biallelic mutation (inactivation)
somatic biallelic mutation
updated 21 months ago by ▴ 160 • written 21 months ago by ▴ 710
0
votes
2
replies
428
views
Violation of Independence test for differential methylation (DM)
methylation differential methylation
2.0 years ago by CY ▴ 710
3
votes
3
replies
1.0k
views
Treat methylation as binary or continuous signal when detecting DMR?
methylation
2.5 years ago by CY ▴ 710
5
votes
1
reply
961
views
Is definition of differentially methylated region (DMR) biologically meaningful?
methylation DMR
updated 2.5 years ago by 2.9k • written 2.5 years ago by ▴ 710
0
votes
2
replies
885
views
Defining methylation level of CpG island
methylation CpG island
2.5 years ago by CY ▴ 710
0
votes
3
replies
602
views
How to derive sequence of novel transcript identified by Cufflinks
transcript RNA-Seq
2.6 years ago by CY ▴ 710
0
votes
0
replies
371
views
Did and why recent studies show superior predictive power using methylation data on early cancer detection
methylation cancer detection
2.7 years ago by CY ▴ 710
0
votes
0
replies
519
views
Example code of MCMC on somatic variant calling (site specific error model)
Variant calling
2.8 years ago by CY ▴ 710
0
votes
0
replies
358
views
Create synthetic data based on general description of molecular characteristic for modeling
next-gen
2.9 years ago by CY ▴ 710
13
votes
9
replies
2.4k
views
Why NB distribution is preferred in RNA-Seq while normal distribution is preferred in microarray?
RNA-Seq Microarray
updated 10 months ago by ★ 4.0k • written 2.9 years ago by ▴ 710
0
votes
2
replies
728
views
Logit-normal distribution to model variation among biological replicates
rMATS alternative splicing distribution
updated 3.0 years ago by 84k • written 3.0 years ago by ▴ 710
0
votes
1
reply
592
views
How does aligner determine strandness when doing alignment
alignment
3.0 years ago by CY ▴ 710
0
votes
4
replies
801
views
Would curated pathway gene set better being weighted than being binary
RNA-Seq enrichment analysis
updated 3.0 years ago by 20 • written 3.2 years ago by ▴ 710
0
votes
3
replies
624
views
Distinguishing real RNA-editing event from sequencing artifact due to reverse transcription
RNA-editing sequencing artifact
3.1 years ago by CY ▴ 710
1
vote
2
replies
870
views
Detection of CNV(InDel) of intermediate size
CNV InDel
21 months ago by CY ▴ 710
2
votes
3
replies
697
views
Identifying zygosity of somatic deletion
CNV
updated 3.1 years ago by ▴ 400 • written 3.1 years ago by ▴ 710
0
votes
3
replies
726
views
In PCA on RNA-Seq data, what does Gaussian distribution refer to?
RNA-Seq PCA Gaussian
updated 3.2 years ago by 103k • written 3.2 years ago by ▴ 710
0
votes
2
replies
711
views
Does variant enrichment analysis make sense?
enrichment analysis somatic variant expression
3.3 years ago by CY ▴ 710
6
votes
6
replies
898
views
Arm-level SCNA does not change mRNA expression level?
CNV SCNA expression
3.3 years ago by CY ▴ 710
2
votes
7
replies
901
views
Why can we still be able to continuously discover new cancer driver bioinformatically these days?
driver gene cancer
3.3 years ago by CY ▴ 710
1
vote
0
replies
412
views
Method to detect genome doubling
CNV genome doubling
3.4 years ago by CY ▴ 710
1
vote
5
replies
768
views
Composition of low mappable region in human genome
mappability repetitive region homologous region
updated 3.4 years ago by 20 • written 3.4 years ago by ▴ 710
0
votes
0
replies
475
views
Any absolute quantification method for detection of polyploidy tumor sample
PCR RNA-Seq
3.4 years ago by CY ▴ 710
1
vote
2
replies
961
views
How splice-aware aligner (RNA-Seq) deal with long gap (intron) penalty
RNA-Seq STAR alignment hisat tophat
updated 3.4 years ago by 20 • written 3.5 years ago by ▴ 710
1
vote
3
replies
664
views
How does base quality / mapping quality affect germline calling
haplotypecaller germline calling MAPQ
3.4 years ago by CY ▴ 710
0
votes
4
replies
959
views
non-reference allele didn't be called into vcf by HC
haplotypecaller vcf
updated 3.5 years ago by 84k • written 3.5 years ago by ▴ 710
0
votes
1
reply
715
views
Dispersion shrinkage in DESeq2: LOESS instead of negative binomial based GLM?
RNA-SEQ DESeq
3.5 years ago by CY ▴ 710
1
vote
5
replies
672
views
Archieve of homologous nucleotide sequence across genome
sequence
updated 3.6 years ago by ▴ 130 • written 3.6 years ago by ▴ 710
0
votes
0
replies
834
views
XHMM calls CNV on a number of normal samples
CNV XHH
3.6 years ago by CY ▴ 710
0
votes
9
replies
1.2k
views
Library size normalization during CNV calling from genomically doubled tumor tissue
CNV
updated 3.6 years ago by ▴ 550 • written 3.6 years ago by ▴ 710
6
votes
5
replies
911
views
Noisy CNV background in old FFPE sample
CNV FFPE
updated 3.7 years ago by ★ 2.8k • written 3.7 years ago by ▴ 710
1
vote
3
replies
658
views
Effect size in power analysis when dealing with Poisson based variant caller
variant calling
updated 3.7 years ago by ▴ 550 • written 3.7 years ago by ▴ 710
0
votes
0
replies
931
views
Difference between mpileup and HaplotypeCaller -ERC BP_RESOLUTION
variant calling haplotypecaller mpileup
3.7 years ago by CY ▴ 710
3
votes
7
replies
1.0k
views
Why methylation sequencing requires much less sequencing depth than DNA-Seq?
methylation WGBS
updated 3.7 years ago by 8.2k • written 3.7 years ago by ▴ 710
18
votes
4
replies
1.1k
views
Why do so many biomarker based classifiers claim high accuracy but rarely used in clinical setting?
biomarker
3.8 years ago by CY ▴ 710
0
votes
1
reply
775
views
Mutated gene based pathway enrichment
enrichment mutation
updated 3.8 years ago by ▴ 990 • written 3.8 years ago by ▴ 710
0
votes
0
replies
654
views
Why seed and fuzzy-search in MIGEC?
MIGEC MUI tcr
3.9 years ago by CY ▴ 710
26
votes
17
replies
6.7k
views
Why can't use t-test for differential expression (negative binomial distribution assumed)
RNA-Seq
updated 3.9 years ago by 13k • written 3.9 years ago by ▴ 710
2
votes
12
replies
1.5k
views
Multiple testing correction issue
multiple testing correction
updated 3.9 years ago by 13k • written 3.9 years ago by ▴ 710
0
votes
1
reply
992
views
Tools that make mutation based phylogenetic tree figure
phylogenetic heterogeneity
4.0 years ago by CY ▴ 710
0
votes
0
replies
650
views
intuitive explaination of using HMM for alignment
HMM alignment
4.0 years ago by CY ▴ 710
1
vote
1
reply
1.0k
views
Capturing TCR from cfDNA
TCR cfDNA ctDNA
4.0 years ago by CY ▴ 710
0
votes
0
replies
1.4k
views
TCR-Seq from bulk RNA-Seq data using TRUST
TCR-Seq RNA-Seq TRUST
4.1 years ago by CY ▴ 710
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