wangshun1121
wangshun1121
如题。我查看了一下源代码，发现下面这几行，似乎把绘图数据来源锁定为确诊数据了。 https://github.com/GuangchuangYu/nCov2019/blob/0bf2c0f322dcfc7a4499639a746ff02f4129bae4/R/plot.R#L112 倘若我需要死亡病例或疑似病例，可否调整一下代码，支持这个需求？
## ❓ Questions and Help I added Shannon-Wiener index in my repo https://github.com/wangshun1121/immunarch/blob/master/R/diversity.R usage: ``` div = repDiversity(immdata$data, "shannon") ``` I think Shannon-Wiener index should be included!
I used strelka2 somatic to detect snv. An important SNV is marked as "LowDepth", and here is the variant in ./results/variants/somatic.snvs.vcf.gz: ``` chr4 66361261 . A G . LowDepth SOMATIC;QSS=53;TQSS=1;NT=ref;QSS_NT=28;TQSS_NT=1;SGT=AA->AG;DP=836;MQ=60.00;MQ0=0;ReadPosRankSum=0.23;SNVSB=0.00;SomaticEVS=1.44...
I use strelka2(v2.9) with default parameters (added --exome) to detect variants in panels, there are many variants with low allele frequencies(0.2 were detected, but variants with lower freq are missed....
As was mentioned in #105 , I'd like to share some more details: In our tumor sample, there is a deletion on TP53 at chr17:7574025, as is shown in IGV...
SpeedSeq is a pipline of high efficency. I wonder if it can deal with species other than Human?\ For example: 1. Medical model organisms such mouse, rat, or monkey etc......
如题，大概看了一下制作融合基因列表的jl脚本和文件。脚本仅仅支持hg19或hg38。我理解OpenGene的julia包里这俩人类基因组的外显子信息应该是有来源的，例如gtf文件。那么，我考虑可否通过gtf文件直接来制造候选的融合基因列表呢？
GATK version: gatk-4.2.3 I have two bam files: `Tumor.bam` is cfDNA data, and `Normal.bam` were reads from white blood cells. There's a variant C to G at `chr7:116795782` (hg38), I...
https://github.com/nextflow-io/nextflow/blame/a7f233053cc18b17192ede4c869ea252f23bc8d8/docs/config.md#L1310 I recently read the paragraph 'Process selectors' in [Configuration](https://www.nextflow.io/docs/latest/config.html#process-selectors) section. About `withName`, I tried my nextflow (22.04.5.5708), and found that "If it is included under the alias hello, it...
This is my gtf file for test, saved as 'Test.gtf': ``` 1 StringTie transcript 9182204 9192089 1000 + . gene_id "origin.STRG.178"; transcript_id "origin.STRG.178.1"; reference_id "ENST00000412639"; ref_gene_id "ENSG00000234546"; ref_gene_name "LINC01759"; cov...