Pinned Repositories
awesome-genome-visualization
A list of interesting genome browser or genome-browser-like implementations
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…
Helitron
TE annotation pipeline Helitron Scanner
R_Workshop
Shiny_projects
This repo provides applications that use Shiny framework for interactice data analysis and visualiztion
sine
TE annotation pipeline for scanning SINE elements
sleuth
sleuth is a program for analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto
Kapeel's Repositories
Kapeel/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…
Kapeel/Helitron
TE annotation pipeline Helitron Scanner
Kapeel/sine
TE annotation pipeline for scanning SINE elements
Kapeel/sleuth
sleuth is a program for analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto
Kapeel/awesome-genome-visualization
A list of interesting genome browser or genome-browser-like implementations
Kapeel/Ballgown
Ballgown R package for RNA-seq differential expression analysis
Kapeel/bio_docker_collcetion
Collect docker files for bioinformatics
Kapeel/common_scripts
my bin directory
Kapeel/dirHub
A trackHub configurator with directory structure projection.
Kapeel/docker-builds
A place to put docker build files
Kapeel/docker_gff_utility_scripts
This repositary contains docker file for scripts to get summary statistics from Gff3 files
Kapeel/edta_docker
Extensive de-novo TE Annotator
Kapeel/full-stack-engineering
Lecture slides and other information from my Full Stack Engineering Workshop
Kapeel/Genome_annotation
These are scripts that I use frequently in genome annotation projects. Some of them have evolved awkwardly so the code is difficult to follw
Kapeel/HISAT2
Hisat alignemnt tool
Kapeel/iPlant_workshop
This is a short tutorial on using icommands
Kapeel/jupyter_notebooks
This repo contains details Jupyter notebooks got genomic data analysis
Kapeel/kallisto
Kallisto RNA seq qauntification tool
Kapeel/Maize_Annotation_Jamboree
This repo contains details for the maize anntation jamboree to be held at CSHL
Kapeel/maize_v4_TE_annotation
scripts and intermediate files used to annotate TEs in Jiao et al.
Kapeel/osg-gl-upendra
Kapeel/pfb2017
Kapeel/pysamstats
A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM or BAM file.
Kapeel/R_projects
repo for R scripts
Kapeel/repeatmodeler
RepeatModeler is a de-novo repeat family identification and modeling package.
Kapeel/snigrum
Annotaiton and Iso-seq analysis for snigrum
Kapeel/Statistic-of-sequenced-plant-genome-assemlies
R scripts
Kapeel/SW_carpentary
This is a template for Software Carpentary workshops
Kapeel/titus-blog
My blog.
Kapeel/workshop-template
Template for workshop websites.