RimanB
Research Fellow in Medicine || Dana-Farber Cancer Institute || Harvard Medical School
Dana-Farber Cancer Institute - Harvard Medical SchoolBoston, MA, US
Pinned Repositories
2021-March-Single-Cell-RNA-Seq-Analysis
A workshop for biologists preparing to run their first single-cell RNA Seq experiment. Participants should have some command line and R experience to participate successfully. We recommend our introductory courses for beginners!
2022_QuPath_Scripts
Assorted collection of QuPath scripts, likely between 2022 and 2023
abdiv
Alpha and beta diversity measures for community ecology
alevin-fry
🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.
BART
BART risk predictor (experimental)
Bioinformatics-for-RNA-Seq
A Tufts University Research Technology Workshop
BLEEP
Spatially Resolved Gene Expression Prediction from H&E Histology Images via Bi-modal Contrastive Learning
CytoCommunity
The first computational tool that enables both unsupervised and supervised discovery of tissue spatial domains
DS_scRNA_20240228
Department of Data Science intro to scRNAseq and data preprocessing workshop
DS_seurat_20240313
RimanB's Repositories
RimanB/CancerRiskNet
RimanB/CBW2023_Met_data
Data for CBW 2023 metabolomics workshop
RimanB/glue-jupyter
Glue front-end for the Jupyter ecosystem
RimanB/MAPS
Machine learning for Analysis of Proteomics in Spatial biology
RimanB/Open3DSIM
This code was created by Ruijie Cao and Prof. Peng Xi in Peking University for 3D SIM reconstruction.
RimanB/biocypher
A unifying framework for biomedical research knowledge graphs
RimanB/pycisTopic
pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
RimanB/akoya_webinar_0622
RimanB/scimap
Spatial Single-Cell Analysis Toolkit
RimanB/pdacR
Downloads and prepares public PDAC data for analysis, and provides some basic tools for this analysis.
RimanB/pyimagej
Use ImageJ from Python
RimanB/BLEEP
Spatially Resolved Gene Expression Prediction from H&E Histology Images via Bi-modal Contrastive Learning
RimanB/rap4all
RimanB/glue-genes
glue for genomics and transcriptomics
RimanB/MultimodalPathologySearch
RimanB/deepcell-tf
Deep Learning Library for Single Cell Analysis
RimanB/alphadev
RimanB/CytoCommunity
The first computational tool that enables both unsupervised and supervised discovery of tissue spatial domains
RimanB/cheatsheets-1
Posit Cheat Sheets - Can also be found at https://posit.co/resources/cheatsheets/.
RimanB/machine-learning
RimanB/Intro-to-rnaseq-hpc-salmon-flipped
Introduction to bulk RNA-seq
RimanB/SPIAT
RimanB/spatialdata-io
RimanB/avillachlab-jenkins-dev-release-control
RimanB/R_Mac_Bug_Fixed
RimanB/indra
INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.
RimanB/CellphoneDB
CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
RimanB/Distributed-Something
Run encapsulated docker containers that do... something in the Amazon Web Services infrastructure.
RimanB/BART
BART risk predictor (experimental)
RimanB/scDesign3