Name: Jérémie Kalfon
Type: User
Company: BroadInstitute - PiPle - PasteurInstitute
Bio: ML, data science, bio-informatics, Full Stack dev, Soft Eng,
Twitter: jkobject
Location: Boston - Paris
Blog: https://www.jkobject.com
Jérémie Kalfon's Projects
my slides
Cell type specific enhancer-gene predictions using ABC model (Fulco et al BioArxiv 2019)
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
We are working on the AML pedDep project with DFCi & the BroadInsitute, looking at CRCs and their relation to genomic dependencies
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.
Awesome list of computational biology.
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
Awesome Benchmark of Gene Regulatory Networks
Access public biological ontologies.
Complete Matlab pipeline for large scale calcium imaging data analysis
Computational toolbox for large scale Calcium Imaging Analysis, including movie handling, motion correction, source extraction, spike deconvolution and result visualization.
tumor - cancer cell line alignment
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
ChIP-seq peak-calling, QC and differential analysis pipeline.
A simple filter to annotate and filter somatic variants based on their observed allele counts in ExAC
a faster Contrastive PCA with ability to only output correction vectors.
dalmatian is a collection of high-level companion functions for Firecloud and FISS.
Training and testing of DeepBind models.
A list of deep learning implementations in biology
What you need to process the Quarterly DepMap-Omics releases from Terra
Registry for scverse ecosystem packages (https://scverse.org/packages/#ecosystem)
Edge-Augmented Graph Transformer
Official code repository for GATK versions 4 and up
A list of awesome files for computational biologists
Jkobject website
A data framework for biology.