Bakhtiyor Nosirov's repositories
ACAM
This is the R package ACAM for cell annotation.
FastRNA
FastRNA: Single-cell analysis of atlas-scale data on a laptop
GBmap
Code used to create the core and extended GBmap, including downstream analyses (cell-cell interactions, spatial transcriptomics deconvolution) and how to produce the figures.
ggsignif
Easily add significance brackets to your ggplots
MAGIC
MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological datasets.
multinichenetr
MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data
muon
muon is a multimodal omics Python framework
muscat
Multi-sample multi-group scRNA-seq analysis tools
popsicleR
popsicleR, a flexible R package aimed at providing most of the necessary quality controls and preliminary information for complete and detailed analysis of single cell RNA-seq data.
presto
Fast Wilcoxon and auROC
r2u
CRAN as Ubuntu Binaries
scCATCH
Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
scCATCH_performance_comparison
The source code and results of performance comparison on the detail of the process among scCATCH, CellAssign, Garnett, SingleR, scMap and CHETAH, and CellMatch database
scMiko
R package developed for single-cell RNA-seq analysis. It was designed using the Seurat framework, and offers existing and novel single-cell analytic work flows.
scPipeline
Single-cell analytic toolbox that offers modular workflows for multi-level cellular annotation and user-friendly analysis reports
seurat-wrappers
Community-provided extensions to Seurat
singleCellHaystack
Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).
STAR
RNA-seq aligner
tenx
Pipelines for the analysis of 10x single-cell RNA-sequencing data
testpipeline
A small example pipeline used to test new nf-core infrastructure and common code.
tools
Python package with helper tools for the nf-core community.
TSEscore_ICIs
Calculate the TSE score to predict response to ICIs
WebPlotDigitizer
HTML5 based online tool to extract numerical data from plot images.