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/oracle_trainer
Scripts to automate the training of Augustus, TwinScan, GeneID and SNAP.
lucventurini/pydata-book
Materials and IPython notebooks for "Python for Data Analysis" by Wes McKinney, published by O'Reilly Media
lucventurini/Afs2DxO
lucventurini/bayesembler
A Bayesian method for doing transcriptome assembly from RNA-seq data
lucventurini/bio_corex
Bio CorEx
lucventurini/dammit
just annotate it, dammit!
lucventurini/diamond
Accelerated BLAST compatible local sequence aligner.
lucventurini/gts
Pipeline that filters transcripts in order to train augustus for non-model organisms
lucventurini/hifive
Tools for handling HiC and 5C data
lucventurini/intervene
Fork of intervene at https://bitbucket.org/CBGR/intervene/overview
lucventurini/matplotlib-venn
Area-weighted venn-diagrams for Python/matplotlib
lucventurini/MICA
MIcrobiomes using Compressive Acceleration
lucventurini/mikado-analysis
Analyses and draft of the paper for Mikado.
lucventurini/minimap2
A versatile pairwise aligner for genomic and spliced nucleotide sequences
lucventurini/OrthoFinder
Accurate inference of orthologous gene groups made easy. "OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthologous gene group inference accuracy"
lucventurini/panYeast
Pipeline to generate a yeast pan genome
lucventurini/PhdThesis
MyPhDThesis.
lucventurini/py-upset
A pure-python implementation of the UpSet suite of visualisation methods by Lex, Gehlenborg et al.
lucventurini/pysamstats
A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM or BAM file.
lucventurini/RaschkaML
Notes and code written while studying "Python Machine Learning".