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asi_sig_hackathon

My notebooks to test some tools

bam2fastq

Simple convertor from bam to FASTQ

bcr_tcr_processing_pipeline

BCR/TCR processing pipeline for NGS data

bioconda-recipes

Conda recipes for the bioconda channel.

cardelino

Clone identification from single-cell data

cell2location

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

cellphonedb

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

cellphonedb-data

clonalomics

Python notebooks containing analysis of clonal gene expression, with a bit of proteomics and ATAC for good measure.

cmapfordc

cytotalk

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

dandelion

dandelion - A single cell BCR/TCR V(D)J-seq analysis package for 10X Chromium 5' data

dandelion-demo-files

demo files for sc-dandelion and notebooks accompanying dandelion manuscript

databases_for_vdj

databases for V(D)J-seq

deepcat

Deep Learning Method to Identify Cancer Associated TCRs

ecosystem-packages

Registry for scverse ecosystem packages

genes2genes

Aligning transcriptomic trajectories of single-cell reference and query systems

genotypemixtures

Stitches together genotype clusters from multiple Souporcell results over large single cell genomics experiments

getsra

wrapper bash scripts to download fastq files from SRR

giana

Ultrafast TCR clustering algorithm based on geometric isometry

github-ci

An example GitHub Action (CI) to build a Singularity container

glmmseq

Gene-level general linear mixed model

harmonypy

🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.

hola

Human-like Orthogonal Layout Algorithm

icon

ismart

Highly specific clustering of T cell receptor CDR3s

kelvinny

Kelvin's R package that holds wrapper functions for a number of work things

ktplots

Some tools for plotting single-cell data

ktplotspy

Python library for plotting Cellphonedb results. Ported from ktplots R package.

mgatk

mgatk: mitochondrial genome analysis toolkit