bharatm26 Goto Github PK

2023-12-03-carpentry-online

2d-spot-plot

2D Spot plot

aucell

AUCell: score single cells with gene regulatory networks

awesome-deep-learning-single-cell-papers

awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

azimuth

A Shiny web app for mapping datasets using Seurat v4

bulk2space

a spatial deconvolution method based on deep learning frameworks, which converts bulk transcriptomes into spatially resolved single-cell expression profiles

bulksignalr

BulkSignalR

cci

Evaluation of cell-cell interaction methods by integrating single-cell RNA sequencing data with spatial information

ccnmf

A Coupled-Clone Nonnegative Matrix Factorization Method for Integrating Tumor Single-Cell RNA and DNA Sequencing Data

cellchat

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

cmplot

📊 Circular and Rectangular Manhattan Plot

complex-upset

A library for creating complex UpSet plots with ggplot2 geoms

configs

Config files used to define parameters specific to compute environments at different Institutions

doubletprediction

predict and compare scRNA/snRNA Seq doublets by three methods

downloader

Easy & parallel download of FASTQ files from public repositories (SRA, EGA, GDC)

enhancedvolcano

Publication-ready volcano plots with enhanced colouring and labeling

flowsom

Using self-organizing maps for visualization and interpretation of cytometry data

gpart

R package; Human genome partitioning of dense sequencing data by identifying haplotype blocks

granulator

hdwgcna

High dimensional weighted gene co-expression network analysis

immunedeconv

A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter) and mouse deconvolution methods

infercnvpy

Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.

monopogen

Single Cell Population Genetics and Association Analysis Tool

multivelo

Multi-omic velocity inference

nichenetr

NicheNet: predict active ligand-target links between interacting cells

pygenometracks

python module to plot beautiful and highly customizable genome browser tracks

rnaseq

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

saturn

scawmv