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Inti Pedroso's starred repositories

vcf2diploid

personal genome constructor

Language:JavaNOASSERTION900

mmseq

Haplotype, isoform and gene level expression analysis using multi-mapping RNA-seq reads

Language:C++GPL-2.06800

Seqnature

Seqnature: incorporate SNPs and Indels into a reference genome

Language:Python1500

Confounded

Removing batch effects & confounding effects from data using deep learning

Language:PythonMIT400

RABBIT

A Mathematica pipeline for genetic analysis in multiparental populations

Language:MathematicaAGPL-3.01300

Phylostratigraphy

Pipeline for Phylostratigraphy

Language:PerlApache-2.01200

Neural-Tree

Tensorflow implementation of a Tree

Language:Python3600

janitor

simple tools for data cleaning in R

Language:RNOASSERTION135100

statements

Successful Job Applications and Grants

NOASSERTION64700

SCALE

Allele-Specific Expression by Single-Cell RNA Sequencing

Language:RGPL-3.02800

kleuren

Find bubbles in the Colored de Bruijn Graph to reconstruct phylogenetic trees

Language:C++MIT1100

HeritSeq

Language:RGPL-2.0200

NCRF

Cancer metastasis detection with neural conditional random field (NCRF)

Language:PythonApache-2.074700

pytorch_geometric

Graph Neural Network Library for PyTorch

Language:PythonMIT2032200

HapCUT2

software tools for haplotype assembly from sequence data

Language:CBSD-2-Clause19200

parallel-fastq-dump

parallel fastq-dump wrapper

Language:PythonMIT26000

kmer-db

Kmer-db is a fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, estimating evolutionary relationships, etc.).

Language:C++GPL-3.07400

GDmat

Calculates Additive and Dominance Relationship Matrices

Language:C++300

easyGEN

A suite of packages for quantitative genetics analysis and more!

Language:R600

ezCV

Cross-validation without doing cross validation

Language:C++GPL-3.0300

fastStructure

A variational framework for inferring population structure from SNP genotype data.

Language:PythonMIT12700

prezto

The configuration framework for Zsh

Language:ShellMIT1381900

v

z for vim

Language:Roff44600

mccortex

De novo genome assembly and multisample variant calling

Language:CMIT11000

phylostratr

An R framework for phylostratigraphy

Language:RGPL-3.03300

methyl_diff

Computes probability of two samples being differentially methylated at given genomic position. Uses number of converted and non converted reads.

Language:C300

cactus

Official home of genome aligner based upon notion of Cactus graphs

Language:CNOASSERTION47500

Comparative-Annotation-Toolkit

Language:PythonApache-2.015800

lightnet

🌓 Bringing pjreddie's DarkNet out of the shadows #yolo

Language:CMIT31900

DCGAN-tensorflow

A tensorflow implementation of "Deep Convolutional Generative Adversarial Networks"

Language:JavaScriptMIT713300