Pinned Repositories
borf
BestORF - select best ORF by optimizing the Tukey's Median of the ILPIs of transcripts at each locus
chess3_construction
chessRevisions
chess revision scripts and notebooks
chimFinder
Foreign DNA/RNA integration site detection
ORFanage
Ultra-efficient and sensitive method to search for Open Reading Frames in spliced genomes guided by reference annotation to maximize protein similarity within genes.
SIM2SAM
conversion of raw polyester FASTA output to SAM in genomic coordinates
tiebrush
Summarize and filter read alignments from multiple sequencing samples (taken as sorted BAM files)
translacc
Small independent tracker for the JHU transloc services to keep count of the missed shuttles and the total lateness each day
chess
Comprehensive Human Expressed SequenceS
bolotie
SARS-CoV-2: detecting recombinations in viruses using large data sets with high sequence similarity
alevar's Repositories
alevar/ORFanage
Ultra-efficient and sensitive method to search for Open Reading Frames in spliced genomes guided by reference annotation to maximize protein similarity within genes.
alevar/tiebrush
Summarize and filter read alignments from multiple sequencing samples (taken as sorted BAM files)
alevar/chimFinder
Foreign DNA/RNA integration site detection
alevar/borf
BestORF - select best ORF by optimizing the Tukey's Median of the ILPIs of transcripts at each locus
alevar/chess3_construction
alevar/genomic_scripts
Various small scripts and tools written in various languages to help in genomic analysis
alevar/ORFclust
Transcript clustering
alevar/translacc
Small independent tracker for the JHU transloc services to keep count of the missed shuttles and the total lateness each day
alevar/sam2gtf
Simple converter fromSAM/BAM/CRAM directly into GTF
alevar/apartment-finder
A Slack bot that helps you find an apartment.
alevar/bed2gff
BED-to-GFF3 converter that runs in parallel
alevar/bifrost
Bifrost: Highly parallel construction and indexing of colored and compacted de Bruijn graphs
alevar/bioconda-recipes
Conda recipes for the bioconda channel.
alevar/CHESS_WEB
Web interface for the CHESS annotation.
alevar/chimViz
Visualize retroviral integrations in host genome
alevar/GANlib
Genome Annotation Library
alevar/gclib
GCLib - Genomic C++ library of reusable code for bioinformatics projects
alevar/gens
Gene density computation
alevar/gff
Rust implementation of gff_utils library with modifications
alevar/gffcompare
classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
alevar/gffread
GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
alevar/IRIS
Inferrence of Retroviral Integration Sites
alevar/libBigWig
A C library for handling bigWig files
alevar/nitron
RNAseq to annotation
alevar/ORFanage_tests
alevar/python-craigslist
Simple Craigslist wrapper
alevar/rust-bio
This library provides implementations of many algorithms and data structures that are useful for bioinformatics. All provided implementations are rigorously tested via continuous integration.
alevar/sashimi
Sashimi with D3
alevar/SPIT
DTU analysis tool inspired by llamas
alevar/upsetjs
😠 UpSet.js - a set visualization library for rendering UpSet Plots (a JavaScript re-implementation of UpSet(R) by Lex et al), Euler Diagrams, Venn Diagrams, and Karnaugh Maps