Pinned Repositories
abra2
ABRA2 forked from the original and modified for my own needs. Credit due to original authors of the paper.
alapy_arc
ALAPY COMPRESSOR: FASTQ lossless compressor
allelicbalancechecker
AMM21
Command-line tool to run Abstract Mediation Model (Weiner et al 2022, AJHG)
auspice.us
BC-store
breakdancer
SV detection from paired end reads mapping
CancerVar
Clinical interpretation of somatic mutations in cancer
ROHMMCLI
ROHMMCLI - Flexible HMM based homozygosity predictor.
VarSight
gokalpcelik's Repositories
gokalpcelik/ROHMMCLI
ROHMMCLI - Flexible HMM based homozygosity predictor.
gokalpcelik/auspice.us
gokalpcelik/ClinSV
Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
gokalpcelik/couplet
gokalpcelik/DEVEA
an interactive shiny application for Differential Expression analysis, data Visualization and Enrichment Analysis of transcriptomics data
gokalpcelik/gatk
Official code repository for GATK versions 4 and up
gokalpcelik/GRIPper
Find non-reference processed pseudogene insertions from discordant read pair mappings
gokalpcelik/herro
HERRO is a highly-accurate, haplotype-aware, deep-learning tool for error correction of Nanopore R10.4.1 or R9.4.1 reads (read length of >= 10 kbps is recommended).
gokalpcelik/htsjdk
A Java API for high-throughput sequencing data (HTS) formats.
gokalpcelik/idep
Integrated Differential Expression and Pathway analysis
gokalpcelik/intervallists
gokalpcelik/LUSH-DNASeq-pipeline
Fast and accurate DNASeq Variant Calling workflow composed of LUSH-toolkits
gokalpcelik/manta
Structural variant and indel caller for mapped sequencing data
gokalpcelik/Maverick
A Mendelian approach to variant effect prediction built in keras
gokalpcelik/mobster
For more details about Mobster please see
gokalpcelik/RBDOOM-3-BFG
Doom 3 BFG Edition with soft shadows, cleaned up source, Linux and 64 bit Support
gokalpcelik/readfish
CLI tool for flexible and fast adaptive sampling on ONT sequencers
gokalpcelik/referencegenomes
gokalpcelik/scarHRD
gokalpcelik/scramble
gokalpcelik/segment-model-spy
An interactive visualization tool for GATK CNV analysis. Displays modeled segments and raw read/allele counts.
gokalpcelik/shallowHRD
This method uses shallow Whole Genome Sequencing (sWGS) and the segmentation of a genomic profile to assess the Homologous Recombination Deficiency of a tumor based on the number of Large-scale Genomic Alterations (LGAs).
gokalpcelik/SpliceAI-lookup
web app for checking SpliceAI scores
gokalpcelik/Spring
FASTQ compression
gokalpcelik/str-analysis
Scripts and utilities related to analyzing short tandem repeats (STRs).
gokalpcelik/tapes
TAPES : a Tool for Assessment and Prioritisation in Exome Studies
gokalpcelik/txt2hpo
Python library for extracting HPO encoded phenotypes from text
gokalpcelik/WisecondorX
WisecondorX — An evolved WISECONDOR
gokalpcelik/WPS-Zotero
An add-on for WPS Writer to integrate with Zotero.
gokalpcelik/xemu
Original Xbox Emulator for Windows, macOS, and Linux (Active Development)