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10kimmunomes_v2

An interactive reference database for immunologists

63_immune_cells

Gene expression profiles of 63 immune cell types

abis

aucell

AUCell: score single cells with gene regulatory networks

batch-computing

Getting Started with Batch Job Scheduling: Slurm Edition

bioc-rnaseq

Analysis and Interpretation of Bulk RNA-Seq Data using Bioconductor

bitfam

BITFAM is a Bayesian approach and platform to infer transcription factor activities within individual cells using single cell RNA-sequencing data. Please see Gao S et al., Genome Research (2021) https://genome.cshlp.org/content/31/7/1296 for details.

bulk-rnaseq-deconvolution-with-scrnaseq

The deconvolution for bulk RNAseq is to have a cell type fraction ratio, say differentational vs un-differential cell fraction in the sample.

cdseq_r_package

CDSeq R Package

cellanneal

User-friendly bulk RNAseq deconvolution using simulated annealing

cellchat

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data

cellphonedb

CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.

cellrank

CellRank for directed single-cell fate mapping

chatgpt-retrieval-plugin

The ChatGPT Retrieval Plugin lets you easily find personal or work documents by asking questions in natural language.

ciml-summer-institute-2023

ciml-summer-institute-2023

class_2023

code_contests

comp_bio_tutorials

coursera-deep-learning-specialization

Notes, programming assignments and quizzes from all courses within the Coursera Deep Learning specialization offered by deeplearning.ai: (i) Neural Networks and Deep Learning; (ii) Improving Deep Neural Networks: Hyperparameter tuning, Regularization and Optimization; (iii) Structuring Machine Learning Projects; (iv) Convolutional Neural Networks;

courses-

Answers for Quizzes & Assignments that I have taken

cytotalk

A novel computational method for inferring cell-type-specific signaling networks using single-cell transcriptomics data for better characterization of cell-cell communication.

df-parallel

Comparison of Dataframe libraries for parallel processing of large tabular files on CPU and GPU.

eigenamin1_scrnaseq_scripts

scRNAseqJupyterScripts

expanse_singularity

human-retina-multiomics

Code for analyzing human retina single-cell data

immuno_notes

Immunology-related bioinformatics data and tools

intro-to-rnaseq-hpc-salmon-flipped

Introduction to bulk RNA-seq

langchain-decoded

A companion guide for the blog post series, LangChain Decoded.

lisbon_single_cell_2021

Repository for the notebooks used in the Single Cell workshop for the Lisbon Summer School 2021

machine-learning-engineering-for-production-public

Public repo for DeepLearning.AI MLEP Specialization