Pinned Repositories
2020plus
Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests
4C-Workflow
Generalized Snakemake workflow for R.4Cker
admixture
Simple accelerated EM implementation of the ADMIXTURE model in R, plus extensions.
AfterQC
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
altair
Declarative statistical visualization library for Python
alview
Alview : Alignment View for BAM files - a fast,portable tool for viewing short reads as native GUI program, command line or via webserver
Anaquin
Statistical analysis of sequins in C++ and R
AnatomyOfMatplotlib
Anatomy of Matplotlib -- tutorial developed for the SciPy conference
lz4
Extremely Fast Compression algorithm
Pipeliner
Pipeliner Program
Biocodings's Repositories
Biocodings/biokit
Bioinformatics in Python
Biocodings/Anaquin
Statistical analysis of sequins in C++ and R
Biocodings/AnatomyOfMatplotlib
Anatomy of Matplotlib -- tutorial developed for the SciPy conference
Biocodings/biobloom
Create Bloom filters for a given reference and then to categorize sequences
Biocodings/DCNet
DCNet — Denoising (DNA) Sequence With a LSTM-RNN and PyTorch & Neural DBG
Biocodings/edlib
Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
Biocodings/ElMaven
LC-MS data processing engine for large-scale metabolomic experiments.
Biocodings/HLA-PRG-LA
Fast HLA type inference from whole-genome data
Biocodings/hotspots
Identifying recurrent mutations in cancer
Biocodings/Immunophenogram
Biocodings/isovar
Abundance quantification of distinct transcript sequences containing somatic variants from cancer RNAseq
Biocodings/kallisto
Near-optimal RNA-Seq quantification
Biocodings/Kart
Kart: A divide-and-conquer algorithm for NGS read mapping with high error tolerance
Biocodings/kourami
Kourami: Graph-guided assembly for HLA alleles
Biocodings/lancet
Microassembly based somatic variant caller for NGS data
Biocodings/lasagne4bio
Biocodings/LotteryPrediction
:full_moon_with_face: Lottery prediction using GA+BF ANN+FL(GeneticAlogrithm+ArtificalNeuralNetwork+FuzzyLogicControl) based on SciPy/NumPy/matplotlib/R/SAS/TensorFlow/Keras
Biocodings/maxquant-pipeline
MaxQuant Automated Pipeline
Biocodings/minimap2
A versatile pairwise aligner for genomic and spliced nucleotide sequences
Biocodings/Neoepitope_Prediction
Biocodings/psp
Python scripts for data processing and analysis of P100 and GCP data
Biocodings/pymzML
pymzML - an interface between Python and mzML Mass spectrometry Files
Biocodings/pyuniprot
Python package to query and analyse UniProt
Biocodings/RNA-seq-analysis
RNAseq analysis notes from Tommy Tang
Biocodings/rnaseq_tutorial
Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.
Biocodings/sequana
Sequana: a set of Snakemake NGS pipelines
Biocodings/sleuth
Differential analysis of RNA-Seq
Biocodings/SUPPA
SUPPA2: Fast quantification of differential splicing
Biocodings/vdjdb-db
Git-based TCR database storage & management. Submissions welcome!
Biocodings/vdjmatch
Matching T-cell repertoire against a database of TCR antigen specificities