Adelia567/Crispr

Crispr is a web app that simplifies the design and analysis of CRISPR guide RNAs, making it accessible for everyone. 🧬 With features like off-target scanning and AI reporting, users can quickly generate and evaluate their gRNA options. 🐙

Language: Python - Size: 158 KB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 0 - Forks: 0

neurogenomics/MotifPeeker

Benchmark Epigenomic Profiling Methods with Motif Enrichment as Key Metric

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CTrierMaansson/DNAfusion

Identification of gene-fusions, including EML4-ALK

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Bioconductor/Organism.dplyr

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Al-Murphy/MungeSumstats

Rapid standardisation and quality control of GWAS or QTL summary statistics

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Bioconductor/OrganismDbi

Software to enable the smooth interfacing of different database packages

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Bioconductor/txdbmaker

A set of tools for making TxDb objects from genomic annotations from various sources (e.g. UCSC, Ensembl, and GFF files)

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Bioconductor/GenomeInfoDb

Utilities for manipulating chromosome names, including modifying them to follow a particular naming style

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Bioconductor/GenomicFeatures

Query the gene models of a given organism/assembly

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Bioconductor/BSgenome

Software infrastructure for efficient representation of full genomes and their SNPs

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Bioconductor/VariantAnnotation

Annotation of Genetic Variants

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Bioconductor/GenomicAlignments

Representation and manipulation of short genomic alignments

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Bioconductor/SummarizedExperiment

A container (S4 class) for matrix-like assays

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Bioconductor/GenomicRanges

Representation and manipulation of genomic intervals

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Bioconductor/Biostrings

Efficient manipulation of biological strings

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hemberg-lab/SC3

A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments

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lima1/PureCN

Copy number calling and variant classification using targeted short read sequencing

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christinehou11/HuBMAPR

R client to discover and retrieve data on HuBMAP Data Portal

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Bioconductor/annotate

Annotation for microarrays

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Bioconductor/KEGGREST

Client-side REST access to KEGG

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Bioconductor/BiocParallel

Bioconductor facilities for parallel evaluation

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Bioconductor/UniProt.ws

R Interface to UniProt Web Services

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crisprVerse/crisprDesign

Comprehensive design of CRISPR gRNAs for nucleases and base editors

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Bioconductor/BiocCheck

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MarioniLab/DropletUtils

Clone of the Bioconductor repository for the DropletUtils package.

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jackgisby/ReducedExperiment

Containers and tools for dimensionally-reduced -omics data

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HSU-HPC/BERT

Batch-Effect Reduction Trees

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uds-helms/BEclear

Correction of batch effects in DNA methylation data

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tatami-inc/beachmat

Clone of the Bioconductor repository for the beachmat package.

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MarioniLab/scran

Clone of the Bioconductor repository for the scran package.

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waldronlab/bugsigdbr

R-side access to published microbial signatures from BugSigDB

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knncolle/BiocNeighbors

Clone of the Bioconductor repository for the BiocNeighbors package.

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waldronlab/curatedMetagenomicData

Curated Metagenomic Data of the Human Microbiome

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systemPipeR/systemPipeShiny

A Shiny framework for workflow management and data visualization

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LTLA/basilisk

Clone of the Bioconductor repository for the basilisk package.

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crisprVerse/crisprScore

On-Target and Off-Target Scoring Algorithms for CRISPR gRNAs

Language: Python - Size: 80.8 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 20 - Forks: 4

LTLA/basilisk.utils

Clone of the Bioconductor repository for the basilisk.utils package.

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shbrief/GenomicSuperSignature

Interpretation of RNAseq experiments through robust, efficient comparison to public databases

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waldronlab/VisiumIO

Import spaceranger output and 10X spatial data

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Bioconductor/GenomicFiles

Distributed computing by file or by range

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waldronlab/doppelgangR

Identify possibly duplicate samples in a list of ExpressionSets

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saezlab/dorothea

R package to access DoRothEA's regulons

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waldronlab/cBioPortalData

Integrate the cancer genomics portal, cBioPortal, using MultiAssayExperiment

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neurogenomics/EpiCompare

Comparison, benchmarking & QC of epigenetic datasets

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federicomarini/GeneTonic

Enjoy your transcriptomic data and analysis responsibly - like sipping a cocktail

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waldronlab/TENxIO

Bioconductor interface to 10X files

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waldronlab/GSEABenchmarkeR

Reproducible GSEA Benchmarking

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waldronlab/CNVRanger

Functionality for CNV analysis

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waldronlab/HMP16SData

16S rRNA Sequencing Data from the Human Microbiome Project

Language: R - Size: 46.6 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 9 - Forks: 6

waldronlab/TCGAutils

Toolbox package for organizing and working with TCGA data

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waldronlab/SingleCellMultiModal

Single Cell multimodal data scripts for downloading datasets

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waldronlab/curatedTCGAData

Curated Data From The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects

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waldronlab/MultiAssayExperiment

Bioconductor package for management of multi-assay data

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waldronlab/curatedOvarianData

The curatedOvarianData package provides data for gene expression analysis in patients with ovarian cancer

Language: R - Size: 371 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 11 - Forks: 4

drisso/SingleCellExperiment

Clone of the Bioconductor repository for the SingleCellExperiment package, see https://bioconductor.org/packages/devel/bioc/html/SingleCellExperiment.html for the official development version.

Language: R - Size: 461 KB - Last synced at: about 1 month ago - Pushed at: about 2 months ago - Stars: 72 - Forks: 20

kullrich/MSA2dist

MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis

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wejlab/TBSignatureProfiler

Profile RNA-seq data using published TB gene signatures

Language: R - Size: 15.6 MB - Last synced at: 7 days ago - Pushed at: 2 months ago - Stars: 12 - Forks: 12

crisprVerse/crisprViz

Visualization of CRISPR guide RNAs (gRNAs)

Language: R - Size: 1.02 MB - Last synced at: about 1 month ago - Pushed at: about 1 year ago - Stars: 9 - Forks: 0

computational-metabolomics/struct

R/Bioconductor package - STRUCT: STatistics in R Using Class Templates

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LTLA/BiocSingular

Clone of the Bioconductor repository for the BiocSingular package.

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schifferl/MultimodalExperiment

Integrative Bulk and Single-Cell Experiment Container

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schifferl/tuberculosis

Tuberculosis Gene Expression Data for Machine Learning

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Bioconductor/DelayedArray

A unified framework for working transparently with on-disk and in-memory array-like datasets

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Bioconductor/Rsamtools

Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import

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waldronlab/terraTCGAdata

TCGA data access on Terra

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waldronlab/MicrobiomeBenchmarkData

Data for benchmarking in microbiome research.

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waldronlab/lefser

R implementation of the LEfSe method

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Bioconductor/BSgenomeForge

Forge your own BSgenome data package

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Bioconductor/BiocBaseUtils

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Bioconductor/S4Arrays

Foundation of array-like containers in Bioconductor

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Bioconductor/HubPub

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Bioconductor/BiocIO

Standard input / output framework for use by Bioconductor packages

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Bioconductor/BiocSet

Representing Different Biological Sets

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Bioconductor/zlibbioc

An R packaged zlib-1.2.5

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Bioconductor/Rhtslib

HTSlib high-throughput sequencing library as an R package

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Bioconductor/RBGL

An interface to the BOOST graph library

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Bioconductor/Icens

NPMLE for Censored and Truncated Data

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Bioconductor/hypergraph

A package providing hypergraph data structures

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Bioconductor/GSEABase

Gene set enrichment data structures and methods

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Bioconductor/graph

graph: A package to handle graph data structures

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Bioconductor/gpls

Classification using generalized partial least squares

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Bioconductor/geneplotter

Graphics related functions for Bioconductor

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Bioconductor/GeneMeta

MetaAnalysis for High Throughput Experiments

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Bioconductor/genefilter

genefilter: methods for filtering genes from high-throughput experiments

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Bioconductor/DynDoc

Dynamic document tools

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Bioconductor/CoCiteStats

Different test statistics based on co-citation.

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Bioconductor/chipseq

chipseq: A package for analyzing chipseq data

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Bioconductor/Category

Category Analysis

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Bioconductor/bioDist

Different distance measures

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Bioconductor/biocViews

Categorized views of R package repositories

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Bioconductor/Biobase

Biobase: Base functions for Bioconductor

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Bioconductor/AnnotationForge

Tools for building SQLite-based annotation data packages

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Bioconductor/AnnotationDbi

Manipulation of SQLite-based annotations in Bioconductor

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Bioconductor/ShortRead

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Bioconductor/ExperimentHubData

Add resources to ExperimentHub

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Bioconductor/IRanges

Foundation of integer range manipulation in Bioconductor

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Bioconductor/S4Vectors

Foundation of vector-like and list-like containers in Bioconductor

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Bioconductor/SplicingGraphs

Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them

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Bioconductor/HDF5Array

HDF5 datasets as array-like objects in R

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Bioconductor/XVector

Foundation of external vector representation and manipulation in Bioconductor

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