Pinned Repositories
Afs2DxO
basenji
Sequential regulatory activity predictions with deep convolutional neural networks.
bayesembler
A Bayesian method for doing transcriptome assembly from RNA-seq data
bio_corex
Bio CorEx
CPC2
Mirror of the CPC2 code.
ei-liftover
Repository to transfer gene models across (sub)genomes and check their coherence.
mikado
Mikado is a lightweight Python3 pipeline whose purpose is to facilitate the identification of expressed loci from RNA-Seq data and to select the best models in each locus.
oracle_trainer
Scripts to automate the training of Augustus, TwinScan, GeneID and SNAP.
pydata-book
Materials and IPython notebooks for "Python for Data Analysis" by Wes McKinney, published by O'Reilly Media
RagTag
Fast reference-guided genome assembly scaffolding
lucventurini's Repositories
lucventurini/mikado
Mikado is a lightweight Python3 pipeline whose purpose is to facilitate the identification of expressed loci from RNA-Seq data and to select the best models in each locus.
lucventurini/CPC2
Mirror of the CPC2 code.
lucventurini/ei-liftover
Repository to transfer gene models across (sub)genomes and check their coherence.
lucventurini/RagTag
Fast reference-guided genome assembly scaffolding
lucventurini/basenji
Sequential regulatory activity predictions with deep convolutional neural networks.
lucventurini/cactus
Official home of genome aligner based upon notion of Cactus graphs
lucventurini/Chiron
A basecaller for Oxford Nanopore Technologies' sequencers
lucventurini/conda-package-handling-feedstock
A conda-smithy repository for conda-package-handling.
lucventurini/DLpipeline
Practical Deep Learning for Genomic Prediction: A Keras based guide to implement deep learning
lucventurini/eager
A fully reproducible and state of the art ancient DNA analysis pipeline.
lucventurini/EDTA
Extensive de-novo TE Annotator
lucventurini/ei-annotation
lucventurini/fastnumbers-feedstock
A conda-smithy repository for fastnumbers.
lucventurini/git-feedstock
A conda-smithy repository for git.
lucventurini/IBSpy
Python library to identify Identical By State regions
lucventurini/lucventurini.github.io
Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes
lucventurini/NanoSim
Nanopore sequence read simulator
lucventurini/pafpy
A lightweight library for working with PAF (Pairwise mApping Format) files
lucventurini/portcullis
Splice junction analysis and filtering from BAM files
lucventurini/pydigree
A python3 package for operations on pedigree and genotype data
lucventurini/python-sortedcontainers
Python Sorted Container Types: Sorted List, Sorted Dict, and Sorted Set
lucventurini/pytritex
Port to Python of Tritex
lucventurini/RaGOO
Fast Reference-Guided Scaffolding of Genome Assembly Contigs
lucventurini/sciluigi
A light-weight wrapper library around Spotify's Luigi workflow system to make writing scientific workflows more fluent, flexible and modular
lucventurini/sqlalchemy-utils
Various utility functions and datatypes for SQLAlchemy.
lucventurini/sqlalchemy-utils-feedstock
A conda-smithy repository for sqlalchemy-utils.
lucventurini/staged-recipes
A place to submit conda recipes before they become fully fledged conda-forge feedstocks
lucventurini/tama
Transcriptome Annotation by Modular Algorithms (for Iso-Seq data)
lucventurini/tensorqtl
Ultrafast GPU-based QTL mapper
lucventurini/TranscriptClean
Correct mismatches, microindels, and noncanonical splice junctions in long reads that have been mapped to the genome