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AwesomeGenomics

Cancer Data Science's go to place for excellent genomics tools and packages
https://github.com/broadinstitute/AwesomeGenomics

Last synced: 5 days ago
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Epigenomics
- ChIPseq and related
  - MACS2
  - MACS2
  - EPIC2
  - RSEG
  - coda
  - CREAM
  - ngsplot
  - epi-corr
  - SUPERmerge - seq read pileup analysis and annotation algorithm for investigating alignment (BAM) files of diffuse histone modification ChIP-seq datasets with broad chromatin domains at a single base pair resolution level
  - nf-core/chipseq
  - pyBigWig
  - deepTools
  - EnrichedHeatmap
  - DeeperBind
  - Basenji
  - ABC model - gene links
  - MACS2 diff binding
  - DeepBind
- Expression
  - crazyhottommy's repo
  - pyGenomeTracks - Epigenomics data
- HiCseq and related
  - HiCExplorer
Awesome awesomeness
- Awesome python
Computational
- Worklow Management
  - Dalmatian
  - Terra
- Dataset Management
  - Taiga
  - taigaR
- Neat python
  - Selene - level deep learning networks
  - nbstripout
  - voila
  - SublimeJEDI
  - functional-python
  - plot in your terminal
  - Itrask
  - ngrock
  - python parser
- Other
- python Basics
  - bokeh
Genomics
- read mapper
  - NextGenMap
- Mutations
  - Mutect1
  - Lancet
  - R
  - Absolute
  - DoAbsolute
  - Strelka
  - Manta
  - DeepVariant
  - py
  - py
  - py
  - OncoKB
  - Oncotator
- Expression
Single Cell
- Others
  - py
- Expression
  - novosparc

Programming Languages

Python 24 R 7 Jupyter Notebook 5 C 4 C++ 4 Cython 2 Lua 1 Nextflow 1 Java 1 Makefile 1

Categories

Epigenomics 21 Genomics 17 Computational 17 Awesome awesomeness 14 Single Cell 2

Sub Categories

ChIPseq and related 18 Awesome python 14 Mutations 13 Neat python 9 Expression 6 Other 3 Dataset Management 2 Worklow Management 2 python Basics 1 read mapper 1 HiCseq and related 1 Others 1

Keywords

python 14 awesome 8 bioinformatics 7 awesome-list 6 data-science 5 machine-learning 5 jupyter-notebook 4 chip-seq 4 deep-learning 4 indels 3 genomics 3 snvs 2 ngs 2 jupyter 2 data-visualization 2 visualization 2 tensorflow 2 clustering 2 rna-seq 2 jupyterlab-extension 2 atac-seq 2 dashboarding 1 functional-programming 1 command-line 1 nbstripout 1 autotrust 1 sampling-methods 1 genomic-data-analysis 1 simulation 1 quantum-chemistry 1 python-chemistry 1 molecular-dynamics 1 interpretable-ml 1 interpretable-machine-learning 1 interpretable-ai 1 interpretability 1 fairness 1 explainable-ml 1 ai-safety 1 tensorflow-tutorials 1 self-driving-cars 1 segmentation 1 neural-networks 1 mit 1 jupyter-notebooks 1 deeplearning 1 deep-rl 1 deep-reinforcement-learning 1 artificial-intelligence 1 plot 1