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100-days-of-ml-code

100-Days-Of-ML-Code中文版

awesome-nlp-sentiment-analysis

:book: 收集NLP领域相关的数据集、论文、开源实现，尤其是情感分析、情绪原因识别、评价对象和评价词抽取方面。

bic-variants_pipeline

BIC@MSKCC Variants Pipeline

cbioportal

cBioPortal for Cancer Genomics

conifer

CoNIFER (Copy Number Inference From Exome Reads) can discover CNVs from exome read-depth data. See Krumm et al., 2012 (Genome Research) for more information.

easy-scraping-tutorial

Simple but useful Python web scraping tutorial code.

gatk-workflows

The new standard in cloud bioinformatics (WDL+Cromwell)

genomicconsensus

PacBio® variant and consensus caller

gwa_tutorial

A comprehensive tutorial about GWAS and PRS

humanid

my first R package just for testing

iap

Illumina analysis pipeline

impact-pipeline

Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay

krona

Interactively explore metagenomes and more from a web browser.

mds-expression

R code for Combining gene mutation with gene expression data improves outcome prediction in myelodysplastic syndromes

mutation-signatures

Create mutation signatures from MAF's, and decompose them into Stratton signatures

mutationalpatterns

R package for extracting and visualizing mutational patterns in base substitution catalogues

oncokb-annotator

Annotates variants in MAF with OncoKB annotation.

paper-zhang2014

Source code from Zhang et al., (2014) Genomic data of avian phylogenomics project. GigaScience 3:26

python-100-days

Python - 100天从新手到大师

rnaseq

RNASeq pipeline

rnaseq_tutorial

Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.

strelka

Strelka2 germline and somatic small variant caller

tcga_example

vcf2maf

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms