gerde Goto Github PK

accucopy

Accucopy is a computational method that infers Allele-specific Copy Number alterations from low-coverage low-purity tumor sequencing Data.

accurity

Accurity is a computational method that infers tumor purity and tumor cell ploidy from tumor-normal WGS (whole exome will probably work too) data by jointly modelling SCNAs and heterozygous germline single-nucleotide-variants (HGSNVs).

antigen.garnish

bamdst

a lightweight bam file depth statistical tool

bamgineer

Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets

bamsurgeon

tools for adding mutations to existing .bam files, used for testing mutation callers

cfmethyl-seq

cfMethyl-Seq code

charr

Contamination from Homozygous Alternate Reference Reads

cnv_facets

Somatic copy variant caller (CNV) for next generation sequencing

codonbert

Repository for mRNA Paper and CodonBERT publication.

conpair

Concordance and contamination estimator for tumor–normal pairs

conv_arithmetic

A technical report on convolution arithmetic in the context of deep learning

ctat-genome-lib-builder

Software used by Trinity CTAT for building CTAT Genome Libs, resource databases shared by Trinity CTAT components

deeplearning-500-questions

深度学习500问，以问答形式对常用的概率知识、线性代数、机器学习、深度学习、计算机视觉等热点问题进行阐述，以帮助自己及有需要的读者。 全书分为18个章节，50余万字。由于水平有限，书中不妥之处恳请广大读者批评指正。 未完待续............ 如有意合作，联系[email protected] 版权所有，违权必究 Tan 2018.06

dl-visuals

Over 200 figures and diagrams of the most popular deep learning architectures and layers FREE TO USE in your blog posts, slides, presentations, or papers.

easyfuse

EasyFuse is a pipeline for accurate fusion gene detection from RNA-seq data.

facets

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

forestploter

Draw forestplot in R

geomlime

ggplot geom_lime()

gerde.github.io

Gerde's blog

gffio

gganatogram

Create anatograms using ggplot2

ggrastr

Raster geoms for ggplot2

imgthla

Github for files currently published in the IPD-IMGT/HLA FTP Directory hosted at the European Bioinformatics Institute

integrate-neo

linearfold

The new source code of the LinearFold, linear-time prediction for RNA secondary structures

mantis

Microsatellite Analysis for Normal-Tumor InStability

methylextract

High-quality methylomes

patchwork

The Composer of ggplots

prtpy

Number partitioning in Python