319 Open source projects that are alternatives of or similar to MultiAssayExperiment

Provide R access to the NCI Genomic Data Commons portal.

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Interactive R package to quantify, analyse and visualise alternative splicing

📓Notebook of Climente-González et al. (2017), The Functional Impact of Alternative Splicing in Cancer.

Mandrake 🌿/👨‍🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding

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Large genome reassembly based on Hi-C data, continuation of GRAAL

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CUT&RUN and CUT&Tag data processing and analysis

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

Representation and manipulation of genomic intervals

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Finds SNP sites from a multi-FASTA alignment file

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simple viewer for variant call format using htslib

A fast tool for hybrid genome assembly of long and short reads

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Examples to get started with IBM Functional Genomics Platform

use the noise

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DriverPower

Analysing Capture Seq Count Data

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

Explore rearrangements and copy-number amplifications in a cancer genome

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences

LRSDAY: Long-read Sequencing Data Analysis for Yeasts

Nextflow basic tutorial for newbie users

mity: A highly sensitive mitochondrial variant analysis pipeline for whole genome sequencing data

Consensus calling (or "reference assisted assembly"), chiefly of ancient mitochondria

A R framework for pipeline benchmarking, with application to single-cell RNAseq

Modeling and correcting fragment sequence bias for RNA-seq

a pileup library that embraces the huge

DISCOVER co-occurrence and mutual exclusivity analysis for cancer genomics data

Materials on the analysis of microarray expression data; focus on re-analysis of public data ( http://tinyurl.com/cruk-microarray)

Contribute Packages to Bioconductor

Performs memory-efficient reservoir sampling on very large input files delimited by newlines

ntHash implementation in Rust

Genome Annotation Without Nightmares

A course on Analysing Next Generation (/High Throughput etc..) Sequencing data using Bioconductor

Bead-based single-cell atac processing

A bioinformatics API and web-app to integrate multi-omics datasets & interface with public databases.

Biopython Jupyter Notebook tutorial to characterize a small genome

Phage-Host Interaction Search Tool

A Snakemake workflow to process single samples or cohorts of paired-end sequencing data (WGS or WES) using trim galore/bwa/GATK4/parabricks.