jblancoheredia

jblancoheredia's Stars

• brentp/bwa-meth

  fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome

  Language:Python13953

• xmu-xiaoma666/External-Attention-pytorch

  🍀 Pytorch implementation of various Attention Mechanisms, MLP, Re-parameter, Convolution, which is helpful to further understand papers.⭐⭐⭐

  Language:Python11.1k1.9k

• jblancoheredia/genomic_immune_tnbc_2024

  Public repository: Nat. Commun. Blanco-Heredia, Souza, Trincado et al, 2024

  Language:Jupyter Notebook1

• dariober/cnv_facets

  Somatic copy variant caller (CNV) for next generation sequencing

  Language:R6715

• Significant-Gravitas/AutoGPT

  AutoGPT is the vision of accessible AI for everyone, to use and to build on. Our mission is to provide the tools, so that you can focus on what matters.

  Language:Python164k43.5k

• ShixiangWang/copynumber

  The "copynumber" R package with support for hg38

  Language:R146

• amf71/ECLIPSE

  Language:R101

• ponnhide/pyCircos-examples

  Example notebooks of pyCircos

  Language:Jupyter Notebook2610

• bell-avery/cnv_cancer_figures

  code for figure 2 of the cancer/copy number project for BIO 465

  Language:Jupyter Notebook2

• CodingBash/CNV-Clinical-Preprocessing

  Subset of scripts created during the CSHL URP 2018. Developing method to extract predictive biomarkers from PDAC patient derived organoids. Using COREs from CNV and WES data from pancreatic tumor organoids to predict chemotherapeutic drug response. This repository investigates copy number preprocessing tools and also preprocesses genomic features for ML analysis.

  Language:Jupyter Notebook3

• aleksmllr/Get-Genotyping-Calls-for-CNVs

  Helped a grad student in my lab with a data processing problem he had regarding CNV genotyping calls for 4444 CNVs spread across 96 samples.

  Language:Jupyter Notebook2

• shoroukKB/CNV-detection-using-machine-learining

  Each significant copy number variation(CNV) in the human genome is related to a specific disease. So, in this project the aim to detect significant CNV using machine learning.

  Language:Jupyter Notebook2

• wdecoster/NanoPlot

  Plotting scripts for long read sequencing data

  Language:Python40048

• tjiangHIT/cuteSV

  Long read based human genomic structural variation detection with cuteSV

  Language:Python23733

• HKU-BAL/Clair3

  Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

  Language:Python22627

• nanoporetech/pipeline-structural-variation

  Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data

  Language:Python11116

• malonge/CallSV

  A long-read SV calling pipeline

  Language:Shell91

• leofountain/FusionHunter

  Identifying fusion transcripts using paired-end RNA-seq

  Language:C2

• riverlee/viewFusion

  View fusion event by circos plot

  105

• JustinChu/JupiterPlot

  A Circos-based tool to visualize genome assembly consistency

  Language:Perl6611

• ponnhide/pyCircos

  python Circos

  Language:Python31966

• Irrationone/clonal-lohhla

  Subclonal determination of HLA LOH

  Language:Python3

• vanallenlab/comut

  CoMut is a Python library for visualizing genomic and phenotypic information via comutation plots

  Language:Python8623

• rhshah/IMPACT-Pipeline

  Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay

  Language:Perl559

• cortes-ciriano-lab/telomere_fusions

  Code to call telomere fusions using DNA sequencing data

  Language:R4

• cancerit/telomerecat

  Telomerecat: The telomere computational analysis tool

  Language:Python165

• hartwigmedical/hmftools

  Various algorithms for analysing genomics data

  Language:Java17956

• MathOnco/NeoPredPipe

  Neoantigens prediction pipeline for multi- or single-region vcf files using ANNOVAR and netMHCpan.

  Language:Python9927