Kapeel

Pinned Repositories

awesome-genome-visualization
A list of interesting genome browser or genome-browser-like implementations
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docker_ltr_retriever
Docker file LTR_retriever accurately identifies and annotates LTR retrotransposons; LAI evaluates the continuity of genome assemblies. https://www.ncbi.nlm.nih.gov/pmc/arti…
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Helitron
TE annotation pipeline Helitron Scanner
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R_Workshop
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Shiny_projects
This repo provides applications that use Shiny framework for interactice data analysis and visualiztion
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sine
TE annotation pipeline for scanning SINE elements
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sleuth
sleuth is a program for analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto
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Kapeel's Repositories

Kapeel/R_Workshop
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Kapeel/Shiny_projects
This repo provides applications that use Shiny framework for interactice data analysis and visualiztion
Language:R1 2 02
Kapeel/awesome-pipeline
A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin
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Kapeel/Ballgown_shinyapp
This repo provides RNA seq differential expression package Ballgown as a Shiny framework for interactive data analysis and visualization
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Kapeel/bcantarel.github.io
NGS Summer BootCamp 2016
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Kapeel/bioconda-recipes
Conda recipes for the bioconda channel.
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Kapeel/cyverse-sdk
A resource for CyVerse developers
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Kapeel/cyverse_agave_apps
A collection of files related to Roger Barthelson's Agave API apps available through the Cyverse Discovery Environment.
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Kapeel/Developing_Data_Products
Developing Data Products Course from the Johns Hopkins Data Science Lab
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Kapeel/encoded
Metadata database for ENCODE 3
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Kapeel/gffcompare
compare and evaluate the accuracy of RNA-Seq transcript assemblers (Cufflinks, Stringtie).
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Kapeel/hisat2-stringtie-ballgown
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Kapeel/imdb-odsc
D3 workshop for ODSC using IMDB dataset
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Kapeel/interactive_mpl_tutorial
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Kapeel/iPlant-basic-scripts
My place for various, simple wrapper scripts
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Kapeel/ipyvolume
3d plotting for Python in the Jupyter notebook based on IPython widgets using WebGL
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Kapeel/long-rna-seq-pipeline
STAR based ENCODE Long RNA-Seq processing pipeline
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Kapeel/MAKER_Shiny_AED
shiny app for AED score distribution
Kapeel/oneliners
Useful bash one-liners for bioinformatics.
Kapeel/RNA-seq-analysis
RNAseq analysis notes from Tommy Tang
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Kapeel/RNA_seq_apps
RNA seq workflow built using agave API to integrate the apps on CyVerse Cyberinfrastructure
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Kapeel/rnaseq_tutorial
Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.
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Kapeel/Sailfish
Sailfish: Rapid Alignment-free Quantification of Isoform Abundance
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Kapeel/Salmon
This a docker file for Salmon RNA quantification tool
Kapeel/Salmon_DE
Updated Salmon app for CyVerse Discovery Environment
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Kapeel/STAR
STAR alignemnt tool
Kapeel/STAR-Stringtie-Ballgown-tutorial
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Kapeel/StringTie
StringTie assembler for RNA seq data
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Kapeel/Tophat_recondition
recondition unmapped bam files from tophat output for further downstream analysis
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Kapeel/tutorials
Explanations and code to analyze common types of big data
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