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cc3d_build_scripts

build scripts for CC3D - used to automatize CC3D buids

ccst

Cell clustering for spatial transcriptomics data with graph neural network

cell2cell

User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins

cell2location

Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)

cellannotator

Automated marker-based annotation of cell types

cellcall

inferring cell-cell communication from scRNA-seq of ligand-receptor

cellchat

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

cellclassificationmachinelearning

Single Cell Classification using RNA-seq data and Supervised Learning Algorithms

cellcutter

Create thumbnails of cells in a given image.

cellnopt

Training of logic models of signalling networks using prior knowledge networks and perturbation data.

cellnoptr

Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data.

cellphonedb

cellsignal-cell-image-analysis

Disentangling biological signal from experimental noise in cellular images.

cellsignalanalysis

Identify major cellular signals in bulk transcriptomes

cellsnp

Pileup biallelic SNPs from single-cell and bulk RNA-seq data

cellsort

This toolbox includes routines for using principal component analysis (PCA)

cellxgene_vip

Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format. It also performs differential gene expression analysis and provides a Command Line Interface (CLI) for advanced users to perform analysis using python and R.

celseq2

Generate the UMI count matrix from CEL-Seq2 sequencing data

cfdna

Analysis of epigenetic signals captured by fragmentation patterns of cell-free DNA

cfret_data

Image-based analysis of cardiac fibroblast datasets to uncover proprietary drug impact on reversing fibrosis

cgview-builder

cgview-js

CGView.js creates interactive circular and linear genome maps.

chatgpt-wrapper

API for interacting with ChatGPT and GPT4 using Python and from Shell.

cheminformatics

Facilitates searching, screening, and organizing large chemical databases

chempy

⚗ A package useful for chemistry written in Python

cmsc702

Repo for Computational Systems Biology and Functional Genomics @ University of Maryland, College Park

cobrapy

COBRApy is a package for constraint-based modeling of metabolic networks.

commot

compbiology-biophysics

It's an general repository containing multiple script for several task into computational biophysics or biology.

compsysbio

Computational Systems Biology course material