boevalab Goto Github PK

accanalysiscode

Code for the CIMP in ACC paper

ans_supplementary_information

atract

ATraCT: Abnormal Transcript Caclulation Tool

cansig

Discovering de novo shared transcriptional programs in single cancer cells

cansig-integration

cansig-supplementary-information

This repository supplements the CanSig tool (https://github.com/boevaLab/cansig), providing additional information on performed experiments.

chipin

ChIP-seq Intersample Normalization

chipseqreadsimulator

ChIPseqReadSimulator: a tool to simulate ChIP-seq signal

cimp_etiology_oncogenic_transformation

Supporting code for the analysis in "Deciphering the etiology and role in oncogenic transformation of the CpG island methylator phenotype (CIMP): a pan-cancer analysis

crcpolyp

Supporting code for Identification of early DNA methylation field cancerization in normal colonic mucosa in patients with adenomas and neoplastic lesions

freec

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

group_lasso_and_multitask

hmcan

hongzhelabro

This is the code collection for Hongzhe Li's Lab rotation project

infercnvpy

Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.

latte

Data analysis of latent representations

lily

Detection of super-enhancers in cancer data

mastertf

multi-omics-noise-resistance

More data, more problems? On noise resistance in multi-omics cancer survival models

multi-task-side-channel

nsclc_patterns

oncocnv

ONCOCNV - a package to detect copy number changes in Targeted Deep Sequencing and Exome-seq data

quantumclone

Clonal reconstruction from HTS data

scalop

Single Cell Analysis Operations

sci

sparsesurv

splattersim

a package to simulate cancer single cells with joint CNV profiles based on Splatter

survboard

sv-bay

Detection of structural variants in cancer mate-pair and paired-end data

teaching

Teaching materials