bit-vs-it Goto Github PK

celligner_ms

Code related to the Celligner manuscript

cellot

Learning Single-Cell Perturbation Responses using Neural Optimal Transport

cellrank

CellRank is a toolkit to uncover cellular dynamics based on Markov state modeling of single-cell data.

cellxgene

An interactive explorer for single-cell transcriptomics data

chimerate

A pipeline to detect chimeric transcripts derived from genes and transposable elements.

chip-seq_notes

Notes on ChIP-seq and other-seq-related tools

chipin

ChIP-seq Intersample Normalization

chippipes

Pipelines for ChIP-seq / CUT&RUN / CUT&Tag etc. analysis

chromgene

Gene-Based Modelling of Epigenomic Data

chromothripsis-gene-amp-cancer

Code associated with publication "Chromothripsis drives the evolution of gene amplification in cancer"

cicero

CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data.

circacompare

circdna

Pipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from cancer and other eukaryotic cells.

circle_finder

Micro DNA identification

circlehunter

A pipeline for identifying complex ecDNA using ATAC-Seq data.

cloneid

cloops2

Enhanced and elegant flexible peak/loop/domain -calling and analysis tool for 1D/3D genomic data.

copyscat

Inferring CNV data from single cell ATAC seq

cosg

Accurate and fast cell marker gene identification with COSG

crc_scrnaseq

cscmap

cscMap is a bioinformatics pipeline to search for the RNA chimeras resulted from fusions of the transcripts encoded by the two opposite DNA strands.

cut-runtools-2.0

cytotalk

A computational method for de novo construction of cell type-specific signaling networks using single-cell transcriptomics data to characterize cell-cell communication.

dase

R package used to category and ranking super-enhancer (SE) subtle differences in two conditions.

deconpeaker

a deconvolution model to identify cell types based on chromatin accessibility in ATAC-Seq data of mixture samples

deepdegron

Deep learning model to predict degron sequences

deepmind-research

This repository contains implementations and illustrative code to accompany DeepMind publications

dendro

Genetic Heterogeneity Profiling by Single Cell RNA Sequencing

dgtac

Differential Gene Targets of Accessible Chromatin

digdriver

Flexible and efficient tests for evidence of positive selection anywhere in the cancer genome.