idealInteractive Differential Expression AnaLysis - DE made accessible and reproducible
Stars: ✭ 24 (+50%)
Protocols-4pubMulti-omics analysis protocols by Lyu.
Stars: ✭ 37 (+131.25%)
GGR-cwlCWL tools and workflows for GGR
Stars: ✭ 20 (+25%)
ngs-in-biocA course on Analysing Next Generation (/High Throughput etc..) Sequencing data using Bioconductor
Stars: ✭ 37 (+131.25%)
DEGreportCreate a cromphensive report of DEG list coming from any analysis of RNAseq data
Stars: ✭ 18 (+12.5%)
dolphinnextA graphical user interface for distributed data processing of high throughput genomics
Stars: ✭ 92 (+475%)
pyrpipeReproducible bioinformatics pipelines in python. Import any Unix tool/command in python.
Stars: ✭ 53 (+231.25%)
GREINGREIN : GEO RNA-seq Experiments Interactive Navigator
Stars: ✭ 40 (+150%)
haystack bioHaystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline
Stars: ✭ 42 (+162.5%)
ALPSAnaLysis routines for ePigenomicS data - 🏫 Bioconductor project
Stars: ✭ 13 (-18.75%)
GeneTonicEnjoy your transcriptomic data and analysis responsibly - like sipping a cocktail
Stars: ✭ 66 (+312.5%)
targets-minimalA minimal example data analysis project with the targets R package
Stars: ✭ 50 (+212.5%)
lumberjackTrack changes in data with ease
Stars: ✭ 58 (+262.5%)
ITKSphinxExamplesCookbook examples for the Insight Toolkit documented with Sphinx
Stars: ✭ 48 (+200%)
sunbeamA robust, extensible metagenomics pipeline
Stars: ✭ 143 (+793.75%)
IsoQuantReference-based transcript discovery from long RNA read
Stars: ✭ 26 (+62.5%)
tidysqtidy processing of biological sequences in R
Stars: ✭ 29 (+81.25%)
dropPipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
Stars: ✭ 69 (+331.25%)
MAnorm2MAnorm2 for Normalizing and Comparing ChIP-seq Samples
Stars: ✭ 15 (-6.25%)
Whippet.jlLightweight and Fast; RNA-seq quantification at the event-level
Stars: ✭ 85 (+431.25%)
MToolBoxA bioinformatics pipeline to analyze mtDNA from NGS data
Stars: ✭ 61 (+281.25%)
iDEADifferential expression (DE); gene set Enrichment Analysis (GSEA); single cell RNAseq studies (scRNAseq)
Stars: ✭ 23 (+43.75%)
zellkonverterConversion between scRNA-seq objects
Stars: ✭ 67 (+318.75%)
xcmsThis is the git repository matching the Bioconductor package xcms: LC/MS and GC/MS Data Analysis
Stars: ✭ 124 (+675%)
Topcuoglu ML mBio 2020Best practices for applying machine learning to bacterial 16S rRNA gene sequencing data
Stars: ✭ 21 (+31.25%)
biojupiesAutomated generation of tailored bioinformatics Jupyter Notebooks via a user interface.
Stars: ✭ 96 (+500%)
pypiperPython toolkit for building restartable pipelines
Stars: ✭ 34 (+112.5%)
NGI-RNAseqNextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.
Stars: ✭ 50 (+212.5%)
pychopperA tool to identify, orient, trim and rescue full length cDNA reads
Stars: ✭ 74 (+362.5%)
RepSePReproducible Self-Publishing - Demo Publications in the Most Common Formats
Stars: ✭ 14 (-12.5%)
scCATCHAutomatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
Stars: ✭ 137 (+756.25%)
rmdTemplatesRmarkdown templates for reproducible science
Stars: ✭ 112 (+600%)
circtoolscirctools: a modular, python-based framework for circRNA-related tools that unifies several functionalities in a single, command line driven software.
Stars: ✭ 19 (+18.75%)
snakefiles🐍 Snakefiles for common RNA-seq data analysis workflows.
Stars: ✭ 78 (+387.5%)
mlst checkMultilocus sequence typing by blast using the schemes from PubMLST
Stars: ✭ 22 (+37.5%)
READemptionA pipeline for the computational evaluation of RNA-Seq data
Stars: ✭ 24 (+50%)
reskitA library for creating and curating reproducible pipelines for scientific and industrial machine learning
Stars: ✭ 27 (+68.75%)
ilusA handy variant calling pipeline generator for whole genome re-sequencing (WGS) and whole exom sequencing data (WES) analysis. 一个简易且全面的 WGS/WES 分析流程生成器.
Stars: ✭ 64 (+300%)
tximportImport and summarize transcript-level estimates for gene-level analysis
Stars: ✭ 117 (+631.25%)
open-cravatA modular annotation tool for genomic variants
Stars: ✭ 74 (+362.5%)
awflowReproducible research and reusable acyclic workflows in Python. Execute code on HPC systems as if you executed them on your personal computer!
Stars: ✭ 15 (-6.25%)
TOGATOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or lost.
Stars: ✭ 35 (+118.75%)
r2gA homology-based, computationally lightweight pipeline for discovering genes in the absence of an assembly
Stars: ✭ 49 (+206.25%)
pytaskpytask is a workflow management system which facilitates reproducible data analyses.
Stars: ✭ 57 (+256.25%)
kallistobustoolskallisto | bustools workflow for pre-processing single-cell RNA-seq data
Stars: ✭ 79 (+393.75%)
TransPiTransPi – a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly
Stars: ✭ 18 (+12.5%)
PECAPECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data
Stars: ✭ 31 (+93.75%)
pipeline-pinfish-analysisPipeline for annotating genomes using long read transcriptomics data with pinfish
Stars: ✭ 27 (+68.75%)
BiocStickersStickers for some Bioconductor packages - feel free to contribute and/or modify.
Stars: ✭ 109 (+581.25%)
showyourworkFully reproducible, open source scientific articles in LaTeX.
Stars: ✭ 361 (+2156.25%)
workflowsBioinformatics curated workflows that use Biocontainers tools
Stars: ✭ 18 (+12.5%)
dee2Digital Expression Explorer 2 (DEE2): a repository of uniformly processed RNA-seq data
Stars: ✭ 32 (+100%)
scTCRseqProcessing of single cell RNAseq data for the recovery of TCRs in python
Stars: ✭ 22 (+37.5%)
GSoC-IdeasCloudCV GSoC 2021 Ideas
Stars: ✭ 95 (+493.75%)