jcdaneshmand

jcdaneshmand's Stars

• navinlabcode/copykat

  Language:R21255

• B-UMMI/long-read-catalog

  catalog for long-read sequencing tools

  3211

• rrrlw/visual-tda

  R code associated with preprint proposing flat persistence diagram for better visualization of persistent homology.

  Language:R53

• rrrlw/TDAstats

  R pipeline for computing persistent homology in topological data analysis. See https://doi.org/10.21105/joss.00860 for more details.

  Language:R379

• mdozmorov/scRNA-seq_notes

  A list of scRNA-seq analysis tools

  Language:R635146

• ChandraPedamallu/PathSeq

  We present a customizable computational tool, PathSeq2.0, to enable the discovery and identification of microbial sequences in metagenomic samples. This is a flexible, user-adaptable, pipeline that is easily assembled using a configuration file tailored towards particular sequencing experiment parameters such as type of sequencing library, sample of origin, sequencing technology, host species and library read length. PathSeq2.0 also provides auxiliary tools that facilitate the identification of viral integration sites within the host genome and quantification of microbial abundance in the sample set.

  Language:Java112

• broadinstitute/gatk

  Official code repository for GATK versions 4 and up

  Language:Java1.7k594

• rstudio/renv

  renv: Project environments for R.

  Language:R1k155

• tdaverse/ripserr

  R package porting Ripser-based persistent homology calculation engines from C++ via Rcpp. Currently ports Ripser (Vietoris-Rips complex) and Cubical Ripser (cubical complex).

  Language:C++75

• scikit-tda/ripser.py

  A Lean Persistent Homology Library for Python

  Language:C++27961

• szairis/sakmapper

  Implementation of Mapper Algorithm

  Language:Python1410

• CamaraLab/scTDA

  An object oriented python library for topological data analysis of high-throughput single-cell RNA-seq data

  Language:Python5121

• YosefLab/VISION

  Signature Analysis and Visualization for Single-Cell RNA-seq

  Language:R16032

• Fadeel/miRinGO

  miRinGO: Prediction of GO terms indirectly targeted by human microRNAs

  Language:R1

• andreafeccomandi/bibisco

  Novel writing software

  Language:JavaScript694116

• musescore/MuseScore

  MuseScore is an open source and free music notation software. For support, contribution, bug reports, visit MuseScore.org. Fork and make pull requests!

  Language:C++12.3k2.7k

• Revolutionary-Games/Thrive-Launcher

  Thrive Launcher for installing and automatically updating Thrive

  Language:C#28838

• Revolutionary-Games/Thrive

  The main repository for the development of the evolution game Thrive.

  Language:C#2.9k507

• sachin-101/Machine-Learning-by-Andrew-Ng-Implementation-in-Python

  To help python programmers experiment and learn. All algorithms implemented from scratch in jupyter notebook.

  Language:Jupyter Notebook11821

• psf/black

  The uncompromising Python code formatter

  Language:Python39.2k2.5k

• parrt/dtreeviz

  A python library for decision tree visualization and model interpretation.

  Language:Jupyter Notebook3k333

• shap/shap

  A game theoretic approach to explain the output of any machine learning model.

  Language:Jupyter Notebook22.9k3.3k

• rawpython/remi

  Python REMote Interface library. Platform independent. In about 100 Kbytes, perfect for your diet.

  Language:Python3.5k402

• federicomarini/pcaExplorer

  pcaExplorer - Interactive exploration of Principal Components of Samples and Genes in RNA-seq data

  Language:R5517

• UofLBioinformatics/affyCustomCdf

  R package for creating custom CDF files for Affymetrix arrays

  Language:C++1

• UofLBioinformatics/circDeep

  End-to-End learning framework for circular RNA classification from other long non-coding RNA using multimodal deep learning

  Language:Python2314

• UofLBioinformatics/CSI-UTR

  A pipeline for detecting differential expression of 3-prime UTRs

  Language:Perl31

• UofLBioinformatics/seekCRIT

  seek for circular RNA in transcriptome (tool to identify deferentially expressed circRNAs between two samples)

  Language:Python73

• MaayanLab/biojupies

  Automated generation of tailored bioinformatics Jupyter Notebooks via a user interface.

  Language:HTML10830

• nf-core/rnaseq

  RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

  Language:Nextflow923708