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xiaoqiwang19's Projects

ancestry_pipeline icon ancestry_pipeline

Provides helper scripts for inferring local ancestry, performing ancestry-specific PCA, etc

annotation icon annotation

注释方面的包(主要是各种ID的转换，KEGG或者GO这样的功能注释，基因信息注释，转录本，外显子起始终止等等)

awesome-r icon awesome-r

A curated list of awesome R packages, frameworks and software.

bwa-mem2 icon bwa-mem2

The next version of bwa-mem (WIP; not recommended for production uses at the moment)

calib icon calib

Calib clusters barcode tagged paired-end reads based on their barcode and sequence similarity.

chrpos2rsid icon chrpos2rsid

chrPos2rsID is a script to convert a list of genomics positions in a format: chrno_position_allele1_allele2 to SNP rsIDs. Script will append rsIDs as a column to an existing file. chrPos2rsID is useful for quick conversion of to SNP rsIDs for various downstream analysis and lookups.

cnv_me icon cnv_me

Copy number variation (CNV) caller utilizing BAM files

cnvkit icon cnvkit

Copy number variant detection from targeted DNA sequencing

contra icon contra

Fork of the CONTRA v2.0.4 package found at http://sourceforge.net/projects/contra-cnv/.

copytranslator icon copytranslator

Foreign language reading and translation assistant based on copy and translate.

cutprimers icon cutprimers

curPrimers is a tool for trimming primer sequences from amplicon based NGS reads

delly icon delly

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis

elprep icon elprep

elPrep: a high-performance tool for preparing sequence alignment/map files in sequencing pipelines.

facets icon facets

Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.

fastp icon fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting...)

fastq-pair icon fastq-pair

Match up paired end fastq files quickly and efficiently.

fes icon fes

Code and Resources for "Feature Engineering and Selection: A Practical Approach for Predictive Models" by Kuhn and Johnson

fgbio icon fgbio

Tools for working with genomic and high throughput sequencing data.

freebayes icon freebayes

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

freec icon freec

Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data

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