kmfisch

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University of California, San Diego

La Jolla, CA

compbio.ucsd.edu

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ucsd-ccbb

UCSD-Fisch-Lab

Kathleen Fisch's starred repositories

bioconda-recipes

Conda recipes for the bioconda channel.

Language:ShellMIT1604 95 1883

bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

Language:PythonMIT984 87 3053

goatools

Python library to handle Gene Ontology (GO) terms

Language:PythonBSD-2-Clause759 23 210

bayesian_first_aid

Inside every classical test there is a Bayesian model trying to get out.

Language:R326 56 22

bioinf-python

Python for Bioinformatics

Language:OpenEdge ABLApache-2.0240 29 6

drmaa-python

Python wrapper around the C DRMAA library.

Language:PythonNOASSERTION109 11 54

visJS2jupyter

visJS2jupyter is a tool to bring the interactivity of networks created with vis.js into jupyter notebook cells

Language:Jupyter NotebookMIT78 21 23

VAPr

VAPr: A Python package for NoSQL variant data storage, annotation and prioritization

Language:PythonMIT34 13 24

bjorn

Language:PythonGPL-3.020 10 22

stormseq

STORMSeq: Scalable Tools for Open-source Read Mapping

Language:JavaScriptNOASSERTION19 7 3

abyss-2.0-giab

:baby_bottle: Assemble the Genome in a Bottle sequencing data

Language:Makefile1000

C-VIEW

This software implements a high-throughput data processing pipeline to identify and charaterize SARS-CoV-2 variant sequences in specimens from COVID-19 positive hosts or environments.

Language:PythonMIT9 8 127

cirrus-ngs

Language:PythonMIT8 11 24

Screw

SCREW: A Reproducible Workflow for Single-Cell Epigenomics

Language:RMIT7 10 29

gsia

Gene Set Information Analysis

Language:R7 4 4

jupyter-pathway

Canonical pathway visualization and analysis

Language:Jupyter NotebookMIT500

mali-dual-crispr-pipeline

This repository contains code for the dual-CRISPR screen analysis pipeline developed to analyze results from the dual-CRISPR screening system set up by the labs of Dr. Prashant Mali and Dr. Trey Ideker. The software is developed by Amanda Birmingham and Roman Sasik of the Center for Computational Biology and Bioinformatics at the University of California, San Diego.

Language:PythonMIT4 6 10

OmicsPipe2.0

Language:PythonNOASSERTION300

PipeMaster

Employs the Omics Pipe framework for automated DNA/RNA-seq variant calling and copy number analysis.

Language:RMIT3 20

qiimp

Web application to collect metadata specifications from an experimenter and produce metadata input files with appropriate constraints

Language:Python3 3 174

MPN_atlas_methods

Source code for methods for A Dynamic Pre-Leukemia Stem Cell Atlas of Myeloproliferative Neoplasm Evolution

Language:Jupyter NotebookMIT200

GeneFreq

Shiny app for exploring distributions of genetic variants in cancer

Language:RMIT1 10

StarCluster-Plugins

Language:PythonMIT1 30

omics_pipe_platypus

Language:PythonMIT1 30