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913
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intuitive explaination of using HMM for alignment
HMM alignment
5.8 years ago by CY ▴ 750
1
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1
reply
1.4k
views
Capturing TCR from cfDNA
TCR cfDNA ctDNA
5.8 years ago by CY ▴ 750
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0
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1.7k
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TCR-Seq from bulk RNA-Seq data using TRUST
TCR-Seq RNA-Seq TRUST
5.9 years ago by CY ▴ 750
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0
replies
1.2k
views
Does it make sense to use methylation data for GESA
GESA methylation expression
5.9 years ago by CY ▴ 750
0
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0
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849
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Question regarding deFuse and fusion calling
RNA-Seq fusion deFuse
5.9 years ago by CY ▴ 750
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0
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1.2k
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Why can't solve tumor clonality using simple EM (Gaussian mixture) instead of MCMC(PyClone) or variational Bayes (SciClone)?
Clonality PyClone SciClone
6.0 years ago by CY ▴ 750
4
votes
5
replies
2.7k
views
Is linearity maintained in linear regression of RNA-Seq?
RNA-Seq
updated 18 months ago by 88k • written 6.1 years ago by ▴ 750
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0
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1.2k
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Any method to solve RNA-Seq's non-linearity problem for deconvoluting immune cell?
RNA-Seq deconvolution
6.1 years ago by CY ▴ 750
3
votes
2
replies
2.1k
views
Somatic variant caller
next-gen variant calling somatic
updated 6.1 years ago by 20 • written 7.8 years ago by ▴ 750
3
votes
6
replies
1.2k
views
Transcriptomic profile fluctuation between different time point
RNA-Seq
updated 6.1 years ago by 20 • written 6.2 years ago by ▴ 750
2
votes
6
replies
4.1k
views
Why use LASSO / elastic net in survival regression?
survival analysis LASSO
updated 6.1 years ago by 27k • written 6.1 years ago by ▴ 750
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0
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1.2k
views
Any tools for co-mutation analysis just like WGCNA on co-expression analysis
Mutation Expression
6.1 years ago by CY ▴ 750
50
votes
9
replies
19k
views
7 follow
why PCA for RNA-Seq but tSNE for scRNA-seq?
pca RNA-Seq tSNE scRNA-seq
updated 6.1 years ago by ▴ 160 • written 6.7 years ago by ▴ 750
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3
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1.0k
views
Can remote, but same type, tissue be used as RNA-Seq normal control for tumor study?
RNA-Seq
updated 6.2 years ago by ★ 4.1k • written 6.2 years ago by ▴ 750
13
votes
8
replies
4.8k
views
Why NMF for mutation signature analysis
mutation NMF signature
6.2 years ago by CY ▴ 750
2
votes
5
replies
1.3k
views
Gene expression distribution (non-DE and DE)
RNA-Seq differential expression
updated 6.3 years ago by 88k • written 6.3 years ago by ▴ 750
1
vote
0
replies
4.4k
views
Shannon index vs Simpson index in evaluating TCR diversity
TCR-Seq TCR diversity
6.3 years ago by CY ▴ 750
3
votes
5
replies
1.6k
views
Low VAF (around 7%) mutated gene prevalent in cancer patient (3/4), driver?
mutation VAF driver gene
6.3 years ago by CY ▴ 750
4
votes
4
replies
1.7k
views
Would different enrichment tools result differently by defining pathway differently
RNA-Seq enrichment analysis
6.3 years ago by CY ▴ 750
2
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3
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1.8k
views
Any tools to estimate the relative abundance of immune cell in tumor
RNA-Seq immune fraction absolute estimate
updated 6.3 years ago by 88k • written 6.3 years ago by ▴ 750
1
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0
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1.0k
views
Can any tool distinguishs immune inflammation / immune excluded phenotype?
RNA-Seq TCR-Seq ESTIMATE
6.3 years ago by CY ▴ 750
3
votes
1
reply
3.0k
views
Driver mutation vs biomarker vs recurrent mutation
Driver mutation biomarker mutation VAF
updated 6.3 years ago by 88k • written 6.3 years ago by ▴ 750
0
votes
1
reply
1.2k
views
Why not simple Gaussian model instead of Gaussian mixture for VQSR?
VQSR GATK
updated 6.5 years ago by 20 • written 6.6 years ago by ▴ 750
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6
replies
1.4k
views
Why VarScan always get more somatic variants than other caller
Variant VarScan
6.6 years ago by CY ▴ 750
1
vote
1
reply
1.3k
views
R plot.DNAcopy with x-axis showing chromosome instead of chromosome coordinate
RNA-Seq CNV DNAcopy
6.6 years ago by CY ▴ 750
2
votes
4
replies
2.1k
views
SciClone: Why cluster in non-CN neutral region considering it infers only on CN neutral region
SciClone clonality
6.6 years ago by CY ▴ 750
4
votes
7
replies
4.4k
views
STAR-HT-Seq/featureCount got much more gene expression count than RSEM did
RNA-Seq STAR RSEM HT-Seq gene expression
6.7 years ago by CY ▴ 750
0
votes
0
replies
1.2k
views
Log-odds based filtering and pairHMM alignment during local realignment
GATK mutect Bayes
updated 6.7 years ago by 20 • written 6.8 years ago by ▴ 750
3
votes
3
replies
2.1k
views
Inconsistency of allele depth in BAM and VCF
allele depth bam vcf variant
updated 6.7 years ago by ▴ 600 • written 6.7 years ago by ▴ 750
1
vote
1
reply
2.0k
views
CBS in CNV calling
cnv cbs
updated 6.7 years ago by 88k • written 6.7 years ago by ▴ 750
0
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0
replies
941
views
RNA-Seq: Expression consistency across time point
RNA-Seq expression
6.8 years ago by CY ▴ 750
2
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3
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1.0k
views
Prior probability during SNP calling
SNP
6.8 years ago by CY ▴ 750
4
votes
2
replies
2.6k
views
How 2-channel sequencing chemistry (Next-Seq) distinguish "G" and 'no signal'
Next-Seq QC
updated 6.8 years ago by 105k • written 6.8 years ago by ▴ 750
2
votes
7
replies
1.9k
views
During GO / pathway enrichment analysis, should we exclude genes not expressed in both groups?
RNA-Seq enrichment analysis DE analysis
6.8 years ago by CY ▴ 750
1
vote
6
replies
1.3k
views
one sample from pool shows low quality at the end, why?
fastqc
6.8 years ago by CY ▴ 750
2
votes
6
replies
2.4k
views
call somatic CNV from cfDNA with normal control
cnv somatic cfDNA
6.9 years ago by CY ▴ 750
2
votes
4
replies
2.6k
views
WGS coverage (depth) for CNV detection
WGS CNV
updated 6.9 years ago by ★ 2.8k • written 6.9 years ago by ▴ 750
0
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6
replies
1.9k
views
How representative the solid tumor sample is to that entire tumor lesion in terms of somatic mutation profile
tumor somatic mutation
6.9 years ago by CY ▴ 750
3
votes
4
replies
3.0k
views
Reads aligning in unstranded RNA-Seq library
RNA-SEQ strand alignment
updated 6.9 years ago by 35k • written 6.9 years ago by ▴ 750
15
votes
4
replies
16k
views
what cause poly-G from NextSeq
nextseq
updated 7.0 years ago by ★ 2.5k • written 7.0 years ago by ▴ 750
5
votes
4
replies
2.0k
views
ExAC includes WES of phenotyped population
ExAC SNP population
updated 7.0 years ago by 22k • written 7.0 years ago by ▴ 750
1
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5
replies
2.1k
views
Is DNA or RNA better to get somatic mutation profile for neoantigen estimation?
somatic mutation
updated 7.0 years ago by ▴ 90 • written 7.0 years ago by ▴ 750
5
votes
18
replies
3.7k
views
Infer somatic mutations without normal control
variant calling somatic mutation
updated 7.0 years ago by ▴ 550 • written 7.0 years ago by ▴ 750
1
vote
5
replies
2.4k
views
pipeline for neo-antigen identification
neo-antigen somatic mutation cancer
updated 7.1 years ago by 22k • written 7.1 years ago by ▴ 750
6
votes
8
replies
5.8k
views
Fragment size and insert size
Fragment size sequencing insert size
updated 7.1 years ago by ★ 2.9k • written 7.1 years ago by ▴ 750
1
vote
4
replies
1.7k
views
Why CNV calling using VarScan need two steps of fragments merging?
cnv VarScan copy number variant
updated 7.1 years ago by ▴ 670 • written 7.1 years ago by ▴ 750
10
votes
12
replies
3.3k
views
Can phasing or pre-phase during basecall cause indel?
indel phasing
updated 7.1 years ago by 88k • written 7.1 years ago by ▴ 750
0
votes
0
replies
990
views
PCT_ribosomal base and PCT_intergenic base in standard RNA-Seq
RNA-Seq QC
7.2 years ago by CY ▴ 750
7
votes
6
replies
2.1k
views
Two confusion in bam format
bam alignment sam
updated 7.3 years ago by 105k • written 7.3 years ago by ▴ 750
4
votes
8
replies
3.2k
views
Why perfectly match (150M) records are not primary alignment in SAM
BAM SAM alignment
updated 7.3 years ago by 35k • written 7.3 years ago by ▴ 750
118 results • Page 2 of 3
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