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0
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0
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1.0k
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Does it make sense to use methylation data for GESA
GESA methylation expression
4.3 years ago by CY ▴ 720
0
votes
0
replies
683
views
Question regarding deFuse and fusion calling
RNA-Seq fusion deFuse
4.3 years ago by CY ▴ 720
0
votes
0
replies
980
views
Why can't solve tumor clonality using simple EM (Gaussian mixture) instead of MCMC(PyClone) or variational Bayes (SciClone)?
Clonality PyClone SciClone
4.4 years ago by CY ▴ 720
2
votes
5
replies
2.0k
views
Is linearity maintained in linear regression of RNA-Seq?
RNA-Seq
updated 4.5 years ago by 85k • written 4.5 years ago by ▴ 720
0
votes
0
replies
955
views
Any method to solve RNA-Seq's non-linearity problem for deconvoluting immune cell?
RNA-Seq deconvolution
4.5 years ago by CY ▴ 720
3
votes
2
replies
1.8k
views
Somatic variant caller
next-gen variant calling somatic
updated 4.5 years ago by 20 • written 6.2 years ago by ▴ 720
3
votes
6
replies
754
views
Transcriptomic profile fluctuation between different time point
RNA-Seq
updated 4.5 years ago by 20 • written 4.6 years ago by ▴ 720
2
votes
6
replies
3.4k
views
Why use LASSO / elastic net in survival regression?
survival analysis LASSO
updated 4.5 years ago by 26k • written 4.5 years ago by ▴ 720
0
votes
0
replies
1.1k
views
Any tools for co-mutation analysis just like WGCNA on co-expression analysis
Mutation Expression
4.5 years ago by CY ▴ 720
49
votes
9
replies
16k
views
7 follow
why PCA for RNA-Seq but tSNE for scRNA-seq?
pca RNA-Seq tSNE scRNA-seq
updated 4.5 years ago by ▴ 160 • written 5.1 years ago by ▴ 720
0
votes
3
replies
674
views
Can remote, but same type, tissue be used as RNA-Seq normal control for tumor study?
RNA-Seq
updated 4.6 years ago by ★ 4.0k • written 4.6 years ago by ▴ 720
13
votes
8
replies
3.7k
views
Why NMF for mutation signature analysis
mutation NMF signature
4.6 years ago by CY ▴ 720
1
vote
4
replies
3.4k
views
Any tools for predicting binding affinity between TCR and epitode?
TCR cancer tool prediction
updated 4.6 years ago by ▴ 40 • written 5.0 years ago by ▴ 720
2
votes
5
replies
875
views
Gene expression distribution (non-DE and DE)
RNA-Seq differential expression
updated 4.6 years ago by 85k • written 4.6 years ago by ▴ 720
1
vote
0
replies
4.0k
views
Shannon index vs Simpson index in evaluating TCR diversity
TCR-Seq TCR diversity
4.6 years ago by CY ▴ 720
3
votes
5
replies
1.1k
views
Low VAF (around 7%) mutated gene prevalent in cancer patient (3/4), driver?
mutation VAF driver gene
4.7 years ago by CY ▴ 720
4
votes
4
replies
1.2k
views
Would different enrichment tools result differently by defining pathway differently
RNA-Seq enrichment analysis
4.7 years ago by CY ▴ 720
2
votes
3
replies
1.4k
views
Any tools to estimate the relative abundance of immune cell in tumor
RNA-Seq immune fraction absolute estimate
updated 4.7 years ago by 85k • written 4.7 years ago by ▴ 720
1
vote
0
replies
820
views
Can any tool distinguishs immune inflammation / immune excluded phenotype?
RNA-Seq TCR-Seq ESTIMATE
4.7 years ago by CY ▴ 720
3
votes
1
reply
2.6k
views
Driver mutation vs biomarker vs recurrent mutation
Driver mutation biomarker mutation VAF
updated 4.7 years ago by 85k • written 4.7 years ago by ▴ 720
0
votes
1
reply
1.1k
views
Why not simple Gaussian model instead of Gaussian mixture for VQSR?
VQSR GATK
updated 4.9 years ago by 20 • written 5.0 years ago by ▴ 720
0
votes
6
replies
1.0k
views
Why VarScan always get more somatic variants than other caller
Variant VarScan
5.0 years ago by CY ▴ 720
1
vote
1
reply
1.0k
views
R plot.DNAcopy with x-axis showing chromosome instead of chromosome coordinate
RNA-Seq CNV DNAcopy
5.0 years ago by CY ▴ 720
2
votes
4
replies
1.6k
views
SciClone: Why cluster in non-CN neutral region considering it infers only on CN neutral region
SciClone clonality
5.0 years ago by CY ▴ 720
4
votes
7
replies
3.4k
views
STAR-HT-Seq/featureCount got much more gene expression count than RSEM did
RNA-Seq STAR RSEM HT-Seq gene expression
5.0 years ago by CY ▴ 720
0
votes
0
replies
1.0k
views
Log-odds based filtering and pairHMM alignment during local realignment
GATK mutect Bayes
updated 5.1 years ago by 20 • written 5.2 years ago by ▴ 720
3
votes
3
replies
1.6k
views
Inconsistency of allele depth in BAM and VCF
allele depth bam vcf variant
updated 5.1 years ago by ▴ 600 • written 5.1 years ago by ▴ 720
1
vote
1
reply
1.8k
views
CBS in CNV calling
cnv cbs
updated 5.1 years ago by 85k • written 5.1 years ago by ▴ 720
0
votes
0
replies
812
views
RNA-Seq: Expression consistency across time point
RNA-Seq expression
5.2 years ago by CY ▴ 720
2
votes
3
replies
850
views
Prior probability during SNP calling
SNP
5.2 years ago by CY ▴ 720
4
votes
2
replies
2.2k
views
How 2-channel sequencing chemistry (Next-Seq) distinguish "G" and 'no signal'
Next-Seq QC
updated 5.2 years ago by 103k • written 5.2 years ago by ▴ 720
2
votes
7
replies
1.4k
views
During GO / pathway enrichment analysis, should we exclude genes not expressed in both groups?
RNA-Seq enrichment analysis DE analysis
5.2 years ago by CY ▴ 720
1
vote
6
replies
956
views
one sample from pool shows low quality at the end, why?
fastqc
5.2 years ago by CY ▴ 720
2
votes
6
replies
1.8k
views
call somatic CNV from cfDNA with normal control
cnv somatic cfDNA
5.2 years ago by CY ▴ 720
2
votes
4
replies
2.0k
views
WGS coverage (depth) for CNV detection
WGS CNV
updated 5.3 years ago by ★ 2.8k • written 5.3 years ago by ▴ 720
0
votes
6
replies
1.4k
views
How representative the solid tumor sample is to that entire tumor lesion in terms of somatic mutation profile
tumor somatic mutation
5.3 years ago by CY ▴ 720
3
votes
4
replies
2.4k
views
Reads aligning in unstranded RNA-Seq library
RNA-SEQ strand alignment
updated 5.3 years ago by 34k • written 5.3 years ago by ▴ 720
13
votes
4
replies
11k
views
what cause poly-G from NextSeq
nextseq
updated 5.4 years ago by ★ 2.4k • written 5.4 years ago by ▴ 720
5
votes
4
replies
1.4k
views
ExAC includes WES of phenotyped population
ExAC SNP population
updated 5.4 years ago by 22k • written 5.4 years ago by ▴ 720
1
vote
5
replies
1.6k
views
Is DNA or RNA better to get somatic mutation profile for neoantigen estimation?
somatic mutation
updated 5.4 years ago by ▴ 90 • written 5.4 years ago by ▴ 720
5
votes
18
replies
2.6k
views
Infer somatic mutations without normal control
variant calling somatic mutation
updated 5.4 years ago by ▴ 550 • written 5.4 years ago by ▴ 720
1
vote
5
replies
1.9k
views
pipeline for neo-antigen identification
neo-antigen somatic mutation cancer
updated 5.4 years ago by 22k • written 5.4 years ago by ▴ 720
6
votes
8
replies
4.4k
views
Fragment size and insert size
Fragment size sequencing insert size
updated 5.5 years ago by ★ 2.8k • written 5.5 years ago by ▴ 720
1
vote
4
replies
1.3k
views
Why CNV calling using VarScan need two steps of fragments merging?
cnv VarScan copy number variant
updated 5.5 years ago by ▴ 670 • written 5.5 years ago by ▴ 720
10
votes
12
replies
2.3k
views
Can phasing or pre-phase during basecall cause indel?
indel phasing
updated 5.5 years ago by 85k • written 5.5 years ago by ▴ 720
0
votes
0
replies
854
views
PCT_ribosomal base and PCT_intergenic base in standard RNA-Seq
RNA-Seq QC
5.6 years ago by CY ▴ 720
7
votes
6
replies
1.6k
views
Two confusion in bam format
bam alignment sam
updated 5.7 years ago by 103k • written 5.7 years ago by ▴ 720
4
votes
8
replies
2.5k
views
Why perfectly match (150M) records are not primary alignment in SAM
BAM SAM alignment
updated 5.7 years ago by 34k • written 5.7 years ago by ▴ 720
5
votes
9
replies
1.5k
views
A confusion regarding haplotype
haplotype genotype chromosome allele
5.7 years ago by CY ▴ 720
3
votes
6
replies
2.1k
views
What kind of advantage does PEAR bring?
pear paired end single end
updated 5.7 years ago by 34k • written 5.7 years ago by ▴ 720
116 results • Page 2 of 3
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