jkobject
ML, data science, bio-informatics, Full Stack dev, Soft Eng,
BroadInstitute - PiPle - PasteurInstituteBoston - Paris
Pinned Repositories
depmap_omics
What you need to process the Quarterly DepMap-Omics releases from Terra
genepy
Genepy is an open source utils package covering a range of useful functions for large scale genomics data analysis in python
scPRINT
single cell foundation model for Gene network inference and more
CaImAn
Computational toolbox for large scale Calcium Imaging Analysis, including movie handling, motion correction, source extraction, spike deconvolution and result visualization.
06-10-21-presentation
benGRN
Awesome Benchmark of Gene Regulatory Networks
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
geneformer
scDataLoader
a dataloader to work with large single cell datasets from lamindb
scPRINT
single cell foundation model for Gene network inference and more
jkobject's Repositories
jkobject/geneformer
jkobject/scDataLoader
a dataloader to work with large single cell datasets from lamindb
jkobject/scPRINT
single cell foundation model for Gene network inference and more
jkobject/benGRN
Awesome Benchmark of Gene Regulatory Networks
jkobject/jkobject.github.io
Jkobject website
jkobject/single-cell-transformer-papers
jkobject/AMLproject
We are working on the AML pedDep project with DFCi & the BroadInsitute, looking at CRCs and their relation to genomic dependencies
jkobject/ABC-Enhancer-Gene-Prediction
Cell type specific enhancer-gene predictions using ABC model (Fulco et al BioArxiv 2019)
jkobject/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.
jkobject/awesome-computational-biology
Awesome list of computational biology.
jkobject/awesome-deep-learning-single-cell-papers
jkobject/awesome-foundation-model-single-cell-papers
jkobject/awesome-single-cell
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
jkobject/bionty-base
Access public biological ontologies.
jkobject/celligner
tumor - cancer cell line alignment
jkobject/contrastive
a faster Contrastive PCA with ability to only output correction vectors.
jkobject/deeplearning-biology
A list of deep learning implementations in biology
jkobject/ecosystem-packages
Registry for scverse ecosystem packages (https://scverse.org/packages/#ecosystem)
jkobject/egt
Edge-Augmented Graph Transformer
jkobject/gatk
Official code repository for GATK versions 4 and up
jkobject/genepy
A list of awesome files for computational biologists
jkobject/GRnnData
Awesome GRN enhanced AnnData toolkit
jkobject/lamindb
A data framework for biology.
jkobject/MM_DREAM
Multiple Myeloma recurrence prediction from the DREAM challenge
jkobject/mnnpy
An implementation of MNN (Mutual Nearest Neighbors) correct in python.
jkobject/RNABERT
jkobject/scGPT
jkobject/slamdunk
A Terra and paired End Enabled Slamdunk: Streamlining SLAM-seq analysis with ultra-high sensitivity
jkobject/slamseq
SLAMSeq processing and analysis pipeline
jkobject/sra_tools