valerianilucrezia

valerianilucrezia's Stars

• mistralai/mistral-evals

  Language:Python213

• adamewing/methylartist

  Tools for plotting methylation data in various ways

  Language:Python13010

• whatshap/whatshap

  Read-based phasing of genomic variants, also called haplotype assembly

  Language:Python34140

• bob-carpenter/prob-stats

  Probability and Statistics: a simulation-based introduction. An open-access book.

  Language:TeX30653

• hildensia/bayesian_changepoint_detection

  Methods to get the probability of a changepoint in a time series.

  Language:Jupyter Notebook678213

• georgecresswell/MiMMAl

  Using two-component Gaussian mixture modelling to estimate the major allele distribution in genotying data.

  Language:R3

• cxli233/FriendsDontLetFriends

  Friends don't let friends make certain types of data visualization - What are they and why are they bad.

  Language:R6.4k243

• ucagenomix/sicelore

  Single Cell Long Read is a suite of tools dedicated to Cell barcode / UMI assignment and analysis of highly multiplexed single cell Nanopore long read sequencing data.

  Language:Java7114

• facebookresearch/DomainBed

  DomainBed is a suite to test domain generalization algorithms

  Language:Python1.4k298

• AndrewSpano/Disentangled-Variational-Autoencoder

  PyTorch Implementations of a VAE and a beta-VAE.

  Language:Jupyter Notebook5915

• 1Konny/Beta-VAE

  Pytorch implementation of β-VAE

  Language:Python522126

• theislab/single-cell-tutorial

  Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq analysis: a tutorial"

  Language:Jupyter Notebook1.4k457

• CompEpigen/ezASCAT

  Conveniently perform ASCAT copy-number analysis from Tumor-Normal or Tumor only BAM files in R

  Language:R112

• brentp/mosdepth

  fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

  Language:Nim698100

• bioinform/somaticseq

  An ensemble approach to accurately detect somatic mutations using SomaticSeq

  Language:Python19353

• cortes-ciriano-lab/savana

  Somatic structural variant caller for long-read data

  Language:Python472

• raphael-group/hatchet-paper

  Related to (Zaccaria and Raphael, 2018), the repository contains the simulated data, the results of all methods involved in the comparison, the results of HATCHet on the prostate and pancreas cancer datasets, and all data and analysis related to these last two cancer datasets.

  Language:Python101

• KolmogorovLab/hapdup

  Pipeline to convert a haploid assembly into diploid

  Language:Python9010

• Hannibal046/Awesome-LLM

  Awesome-LLM: a curated list of Large Language Model

  18.5k1.5k

• iamalexkorotin/NeuralOptimalTransport

  PyTorch implementation of "Neural Optimal Transport" (ICLR 2023 Spotlight)

  Language:Jupyter Notebook17619

• Nextomics/NextPolish

  Fast and accurately polish the genome generated by long reads.

  21227

• genome-in-a-bottle/genome-stratifications

  Stratification BED files from the Global Alliance for Genomics and Health (GA4GH) Benchmarking Team and the Genome in a Bottle Consortium. These files can be used as standard resource of BED files for use with GA4GH benchmarking tools such as hap.py to stratify true positive, false positive, and false negative variant calls based on genomic context.

  Language:HTML756

• seanrjohnson/esmologs

  Local homology search powered by ESM-2 language model, foldseek, hhsuite, and hmmer.

  Language:Jupyter Notebook12

• mheinzinger/ProstT5

  Bilingual Language Model for Protein Sequence and Structure

  Language:Jupyter Notebook18115

• crazyhottommy/DNA-methylation-analysis

  DNA methylation analysis notes from Ming Tang

  7935

• buenrostrolab/tss-annotation

  Simple reproducible managment of annotated TSS and gene bodies

  Language:Shell41

• nanoporetech/modkit

  A bioinformatics tool for working with modified bases

  Language:Rust1398

• nanopore-wgs-consortium/NA12878

  Data and analysis for NA12878 genome on nanopore

  Language:Python37592

• Oshlack/JAFFA

  JAFFA is a multi-step pipeline that takes either raw RNA-Seq reads, or pre-assembled transcripts, then searches for gene fusions

  Language:C++8721

• gaolabtools/scNanoGPS

  Single cell Nanopore sequencing data for Genotype and Phenotype

  Language:Python392