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bioinformatics
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294 search results found
Dash
⭐
19,976
Data Apps & Dashboards for Python. No JavaScript Required.
Adam
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966
ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.
Dada2
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428
Accurate sample inference from amplicon data with single nucleotide resolution
Maftools
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400
Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
Canvasxpress
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282
CanvasXpress: A JavaScript Library for Data Analytics with Full Audit Trail Capabilities.
Karyoploter
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278
karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome
Immunarch
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256
🧬 Immunarch: an R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires
Teachingdemos
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216
Bioinformatics related demos and tutorials using the R programming language
Smudgeplot
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200
Inference of ploidy and heterozygosity structure using whole genome sequencing data
Splatter
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195
Simple simulation of single-cell RNA sequencing data
Pecan
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193
The Predictive Ecosystem Analyzer (PEcAn) is an integrated ecological bioinformatics toolbox.
Gwa_tutorial
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184
A comprehensive tutorial about GWAS and PRS
Youtubetutorials
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180
Bioc Refcard
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170
Bioconductor cheat sheet
Bigsnpr
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168
R package for the analysis of massive SNP arrays.
Scde
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163
R package for analyzing single-cell RNA-seq data
Teachingmaterial
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161
Various teaching material
Genomics
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154
A collection of scripts and notes related to genomics and bioinformatics
Shinycircos
⭐
145
an R/shiny application for creation of Circos plot interactively
Itol.toolkit
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137
Helper Functions for Interactive Tree Of Life (iTOL)
Rnaseq Workflow
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133
A repository for setting up a RNAseq workflow
Decontam
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122
Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
Sigminer
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119
🌲 An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R https://shixiangwang.github.io/sigminer/reference/
Msnbase
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115
Base Classes and Functions for Mass Spectrometry and Proteomics
Swne
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100
Similarity Weighted Nonnegative Embedding (SWNE), a method for visualizing high dimensional datasets
Tutorial
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94
Tutorials on machine learning, artificial intelligence, data science with math explanation and reusable code (in python and R)
Nmf
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94
NMF: A Flexible R package for Nonnegative Matrix Factorization
Ucscxenatools
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93
📦 An R package for accessing genomics data from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq https://cran.r-project.org/web/packages/UCSCXenaTo
Workshop
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92
课题组每周研讨会
Rblast
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91
Interface for the Basic Local Alignment Search Tool (BLAST) - R-Package
Snprelate
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90
R package: parallel computing toolset for relatedness and principal component analysis of SNP data (Development version only)
Genomicdatacommons
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80
Provide R access to the NCI Genomic Data Commons portal.
Geoquery
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73
The bridge between the NCBI Gene Expression Omnibus and Bioconductor
Peptides
⭐
71
An R package to calculate indices and theoretical physicochemical properties of peptides and protein sequences.
Startapp
⭐
71
The START App: R Shiny Transcriptome Analysis Resource Tool
Chromvar
⭐
69
chromatin Variability Across Regions (of the genome!)
Singlecellhaystack
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68
Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).
Hyper
⭐
65
An R Package for Geneset Enrichment Workflows
Scatac Pro
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64
A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data
Single Cell Training
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63
SIB course on single cell transcriptomics by mostly using the Seurat pipeline
Graffite
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62
GraffiTE is a pipeline that finds polymorphic transposable elements in genome assemblies and/or long reads, and genotypes the discovered polymorphisms in read sets using genome-graphs.
Ebimage
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62
🎨 Image processing toolbox for R
Mungesumstats
⭐
59
Rapid standardisation and quality control of GWAS or QTL summary statistics
Cmapr
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56
Tools for manipulating annotated data matrices
Palimpsest
⭐
56
An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
Scmerge
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53
Statistical approach for removing unwanted variation from multiple single-cell datasets
Gosemsim
⭐
52
⛳ GO-terms Semantic Similarity Measures
Tftargets
⭐
52
🎯 Human transcription factor target genes.
Protr
⭐
50
🧬 Toolkit for generating various numerical features of protein sequences
Tomicsvis
⭐
50
Transcriptomics Visualization R package.
Slurmr
⭐
50
slurmR: A Lightweight Wrapper for Slurm
Bioinstaller
⭐
50
A comprehensive R package to construct interactive and reproducible biological data analysis applications based on the R platform
Ggvolc
⭐
50
𝐠𝐠𝐯𝐨𝐥𝐜 effortlessly translates differential expression datasets and RNAseq data into informative volcano plots. Highlight genes of interest with unprecedented ease. With just a single line of code, visualize complex datasets, gaining deeper insights and simplifying data representation
Twitter
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48
Code to analyse interesting Twitter data (e.g. conference coverage)
Variancepartition
⭐
48
Quantify and interpret divers of variation in multilevel gene expression experiments
Liger
⭐
47
Lightweight Iterative Gene set Enrichment in R
Biobroom
⭐
47
Tidy up computational biology objects
Easytcga
⭐
45
Make TCGA download and prepare easy!
Covid19 Event Risk Planner
⭐
45
COVID19 risk planner R-Shiny application
Dchic
⭐
44
dcHiC: Differential compartment analysis for Hi-C datasets
Testingpackage
⭐
43
R Package Illustrating Components of an R package for BCB410H - Applied Bioinformatics (2019-2023), University of Toronto, Canada
Sesame
⭐
43
🍪 SEnsible Step-wise Analysis of DNA MEthylation BeadChips
Pato
⭐
42
PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.
Seqarray
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41
Data management of large-scale whole-genome sequence variant calls (Development version only)
Shinychromosome
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38
an R/Shiny application for interactive creation of non-circular plots of whole genomes
Tcc Gui
⭐
37
📊 Graphical User Interface for TCC package
Qtlmap
⭐
36
Portable eQTL analysis and statistical fine mapping workflow used by the eQTL Catalogue
Singscore
⭐
36
An R/Bioconductor package that implements a single-sample molecular phenotyping approach
Homologene
⭐
35
🐭 ↔️ 👫 An r package that works as a wrapper to homologene
Shinygeo
⭐
35
Gene Expression Omnibus Analysis with Shiny 🔬
Antigen.garnish
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35
Nam Genomes
⭐
34
Detailed bioinformatics scripts and methods used in the NAM genome paper.
Partition
⭐
34
A fast and flexible framework for data reduction in R
Wdlrunr
⭐
34
Elastic, reproducible, and reusable genomic data science tools from R backed by cloud resources
Orca
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34
🐳 Genomics Research Container Architecture
Projectreconnect
⭐
34
use bioinformatics to identify/reconnect lost children in China
Dmrichr
⭐
33
A R package and executable for the preprocessing, statistical analysis, and downstream testing and visualization of differentially methylated regions (DMRs) from CpG count matrices (Bismark cytosine reports)
Oxbow
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32
Read specialized NGS formats as data frames in R, Python, and more.
Tailfindr
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32
An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.
Sscclust
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32
simpler single cell RNAseq data clustering
Reductionwrappers
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32
R wrappers to connect Python dimensional reduction tools and single cell data objects (Seurat, SingleCellExperiment, etc...)
Tcr
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31
[DEPRECATED, see https://immunarch.com/] tcR: an R package for immune receptor repertoire advanced data analysis.
Orthogene
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31
🧬 o r t h o g e n e 🧬✨✨✨✨✨✨✨ Interspecies gene mapping✨✨✨✨✨ 🦠 🔁 🌱 🔁 🌳 🔁 🍎 🔁 🍊 🔁 🪱 🔁 🪰 🔁 🐟 🔁 🦎 🔁 🐓 🔁 🦇 🔁 🐄 🔁 🐖 🔁 🐐 🔁 🐎 🔁 🐈 🔁 🐕 🔁 🐁 🔁 🐒 🔁 🦧 🔁 🦍 🔁 🏃♀️
Cytometry Clustering Comparison
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30
R scripts to reproduce analyses in our paper comparing clustering methods for high-dimensional cytometry data
Gtdb Taxdump
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29
GTDB taxonomy taxdump files with trackable TaxIds
Rcpi
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28
Molecular informatics toolkit with a comprehensive integration of bioinformatics and cheminformatics tools for drug discovery.
Csbb Shiny
⭐
28
Computational Suite for Bioinformaticians and Biologists (CSBB) is a RShiny application developed with an intention to empower researchers from wet and dry lab to perform downstream Bioinformatics analysis
Phylostratr
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28
An R framework for phylostratigraphy
Self Study
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28
My Self-Study Room: keep tidy and lightweight
Tidysq
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28
tidy processing of biological sequences in R
Bdvis
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27
Biodiversity data Visualizations in R
Biomart
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27
R package providing query functionality to BioMart instances like Ensembl
Sevenbridges R
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27
Seven Bridges API Client, CWL Schema, Meta Schema, and SDK Helper in R
Candis
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27
🎀 A data mining suite for gene expression data.
Seuratv3wizard
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26
A web-based interactive (wizard style) application to perform a guided single-cell RNA-seq data analysis and clustering based on Seurat v3
Phyloprofile
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26
A phylogenetic profile analysis tool
Omicselector
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26
OmicSelector - Environment, docker-based application and R package for biomarker signiture selection (feature selection) & deep learning diagnostic tool development from high-throughput high-throughput omics experiments and other multidimensional datasets. Initially developed for miRNA-seq, RNA-seq and qPCR.
Admixr
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25
An R package for reproducible and automated ADMIXTOOLS analyses
Jamp
⭐
24
JAMP - Just Another Metabarcoding Pipeline
Vigen
⭐
24
viGEN - A bioinformatics pipeline for the exploration of viral RNA in human NGS data
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