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/DS_scRNA_20240228
Department of Data Science intro to scRNAseq and data preprocessing workshop
RimanB/DS_seurat_20240313
RimanB/iCCA_Diversity
RimanB/NGS-variants-training
GitHub for the SIB courses NGS - Genome variant analysis
RimanB/sanbomics_scripts
scripts and notebooks from sanbomics
RimanB/2024_ISB_workshop_Practical_Methods_in_Spatial-Omics
RimanB/3ca
Code for reproducing the analysis in Gavish et al. "The transcriptional hallmarks of intra-tumor heterogeneity across a thousand tumors".
RimanB/CellProfileLibrary
RimanB/clusterProfiler_protocol
omics data analysis using clusterProfiler ;)
RimanB/CosMx-Analysis-Scratch-Space
This repository is an exploratory resource to accelerate opensource analysis of CosMx® Spatial Molecular Imager (SMI) data. Contained here are and writeups and vignettes addressing a variety of topics discussed when analyzing single-cell spatial data.
RimanB/DGE_analysis_scRNAseq
Approaches for looking at differential expression and differential abundance in scRNA-seq
RimanB/DGE_workshop_salmon_online
RimanB/FastReseg
FastReseg for detection and correction of cell segmentation error based on spatial profile of transcripts.
RimanB/gfoRmula
The gfoRmula package implements the parametric g-formula in R. The parametric g-formula (Robins, 1986) uses longitudinal data with time-varying treatments and confounders to estimate the risk or mean of an outcome under hypothetical treatment strategies specified by the user.
RimanB/GPT4DFCI
A private and secure generative AI tool, based on GPT-4 and deployed for non-clinical use at Dana-Farber Cancer Institute
RimanB/hiepnguyen.github.io
RimanB/InSituType
An R package for performing cell typing in SMI and other single cell data
RimanB/Intro-to-ChIPseq-flipped
RimanB/liana-py
LIANA+: an all-in-one framework for cell-cell communication
RimanB/MedSAM
Segment Anything in Medical Images
RimanB/MGMA_2024
RimanB/openseadragon
An open-source, web-based viewer for zoomable images, implemented in pure JavaScript.
RimanB/openslide
C library for reading virtual slide images
RimanB/pathml
Tools for computational pathology
RimanB/SCOTIA
RimanB/STAMP
Solid Tumor Associative Modeling in Pathology
RimanB/StatsForCompBio
DFCI Department of Data Sciences workshop on Statistics for Computational Biology Projects
RimanB/tiny_python_projects
Code for Tiny Python Projects (Manning, 2020, ISBN 1617297518). Learning Python through test-driven development of games and puzzles.
RimanB/toga
A Python native, OS native GUI toolkit.
RimanB/WSITools
Tools for whole slide image (WSI) processing. Especially for (pairwise) patch extraction, annotation parsing and data preparation for deep learning purposes.