jkobject Goto Github PK

02-02-21-cdspresentation

my slides

06-10-21-presentation

abc-enhancer-gene-prediction

Cell type specific enhancer-gene predictions using ABC model (Fulco et al BioArxiv 2019)

aml-crc-cobinding

Epigenetic co-binding analysis of the of the core regulatory circuitry in AML (leukemia) Orkin Lab & Stegmeyer Lab in partnership with the Cancer Data Science group

amlproject

We are working on the AML pedDep project with DFCi & the BroadInsitute, looking at CRCs and their relation to genomic dependencies

arxiv-sanity-lite

arxiv-sanity lite: tag arxiv papers of interest get recommendations of similar papers in a nice UI using SVMs over tfidf feature vectors based on paper abstracts.

bengrn

Awesome Benchmark of Gene Regulatory Networks

bionty-base

Access public biological ontologies.

ca_source_extraction

Complete Matlab pipeline for large scale calcium imaging data analysis

caiman

Computational toolbox for large scale Calcium Imaging Analysis, including movie handling, motion correction, source extraction, spike deconvolution and result visualization.

celligner

tumor - cancer cell line alignment

chip2crc

from ChiP to Core Regulatory Circuitry explains the steps to go from a chip file to a CRC file from the paper http://www.genome.org/cgi/doi/10.1101/gr.197590.115

chipseq

ChIP-seq peak-calling, QC and differential analysis pipeline.

common_variant_filter

A simple filter to annotate and filter somatic variants based on their observed allele counts in ExAC

contrastive

a faster Contrastive PCA with ability to only output correction vectors.

dalmatian

dalmatian is a collection of high-level companion functions for Firecloud and FISS.

deepbind

Training and testing of DeepBind models.

depmap_omics

What you need to process the Quarterly DepMap-Omics releases from Terra

egt

Edge-Augmented Graph Transformer

gatk

Official code repository for GATK versions 4 and up

geneformer

genepy

A list of awesome files for computational biologists

jkobject.github.io

Jkobject website

lamindb

A data framework for biology.

lanyon

A content-first, sliding sidebar theme for Jekyll.

macs

MACS -- Model-based Analysis of ChIP-Seq

made-mistakes-jekyll

:ghost: Source for my website and blog (Jekyll + Gulp + Netlify)

minimal-mistakes

:triangular_ruler: A flexible two-column Jekyll theme perfect for building personal sites, blogs, and portfolios.

mm_dream

Multiple Myeloma recurrence prediction from the DREAM challenge

mnnpy

An implementation of MNN (Mutual Nearest Neighbors) correct in python.