SigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations. It allows downsizing the generated mutations only to parts for the genome (e.g., exome or a custom BED file). The tool seamlessly integrates with other SigProfiler tools.

✭ 68

python bioinformatics somatic-variants cancer-genomics mutation-analysis mutational-signatures

virtool

Viral infection diagnostics using next-generation sequencing

✭ 36

python HTML bioinformatics web-app diagnostics viral-ngs

lynnlangit

Lynn Langit profile

✭ 46

julia Jupyter Notebook machine-learning bioinformatics cloud-computing

phylonium

♥ Fast and Accurate Estimation of Evolutionary Distances

✭ 18

C++c M4 bioinformatics phylogenetics alignment-free

TCC-GUI

📊 Graphical User Interface for TCC package

✭ 35

r HTML gui bioinformatics rna-seq shiny tcc

BioMedical-NLP-corpus

Biomedical NLP Corpus or Datasets.

✭ 44

nlp natural-language-processing text-mining bioinformatics dataset named-entity-recognition corpus-data medical-informatics

crass

The CRISPR assembler

✭ 30

C++M4 c shell bioinformatics crispr

bigly

a pileup library that embraces the huge

✭ 38

go python bioinformatics genomics

weekly

生信爱好者周刊（每周日发布）

✭ 158

HTML bioinformatics weekly free-journals

awesome-nanopore

A curated list of awesome nanopore analysis tools.

✭ 100

machine-learning bioinformatics nanopore awesome-list

pm4ngs

Project Manager for NGS data analysis

✭ 21

python bioinformatics next-generation-sequencing rnaseq ngs-analysis ngs-pipeline cwl-workflow chipseq chipexo

snp-sites

Finds SNP sites from a multi-FASTA alignment file

✭ 182

c M4 perl C++bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline global-health infectious-diseases

TreeSAPP

A Python package for gene-centric taxonomic and functional classification using phylogenetic placement

✭ 20

python r C++UnrealScript shell Dockerfile bioinformatics phylogenetics microbial-genomics

bac-genomics-scripts

Collection of scripts for bacterial genomics

✭ 39

perl shell science unix opensource bioinformatics annotation genomics ngs sequencing computational-biology microbial-genomics blast microbiology mlst bioperl scripts-collection

pysces

The official PySCeS project source code repository.

✭ 25

python fortran bioinformatics simulation mca console-application steady-state sbml kinetic-modeling

deepsignal

Detecting methylation using signal-level features from Nanopore sequencing reads

✭ 90

python bioinformatics tensorflow methylation epigenetics nanopore-sequencing

CAFE

Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.

✭ 88

C++c perl python Makefile Raku bioinformatics phylogenetics gene-families

rnftools

RNF framework for NGS: simulation of reads, evaluation of mappers, conversion of RNF-compliant data.

✭ 14

python erlang shell Makefile Dockerfile bioinformatics ngs read-simulation mapper-evaluation ngs-format

fastqp

Simple FASTQ quality assessment using Python

✭ 101

python bioinformatics sam fastq nucleotide-plot kmer-distribution

stochpy

StochPy is a versatile stochastic modeling package which is designed for stochastic simulation of molecular control networks

✭ 36

python bioinformatics systems-biology console-application stochastic-simulation-algorithm kinetic-modeling

scaden

Deep Learning based cell composition analysis with Scaden.

✭ 61

python Dockerfile machine-learning bioinformatics rna-seq deep-learning deconvolution single-cell-rna-seq cell-composition-analysis

mageri

MAGERI - Assemble, align and call variants for targeted genome re-sequencing with unique molecular identifiers

✭ 19

java groovy bioinformatics cancer mapping mutation umi variant amplicon exon ctdna

OmicLearn

🧪 🖥 Transparent exploration of machine learning for biomarker discovery from proteomics and omics data

✭ 46

python Jupyter Notebook machine-learning bioinformatics proteomics omics biomarker-discovery

sample

Performs memory-efficient reservoir sampling on very large input files delimited by newlines

✭ 61

c Makefile bioinformatics genomics sampling bed reservoir-sampling

CloudConductor

CloudConductor is a workflow management system that generates and executes bioinformatics pipelines

✭ 13

python Dockerfile workflow cloud bioinformatics pipeline google-cloud

wgdi

WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes

✭ 67

python bioinformatics polyploidy collinearity ancestral-chromosomal-karyotype

biopython-coronavirus

Biopython Jupyter Notebook tutorial to characterize a small genome

✭ 80

Jupyter Notebook bioinformatics genomics jupyter-notebook biopython coronavirus covid-19

TOBIAS

Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal

✭ 128

python cython shell bioinformatics atac-seq footprinting

pdb-tools

A dependency-free cross-platform swiss army knife for PDB files.

✭ 240

python TeX bioinformatics structural-biology pdb protein structural-bioinformatics utrecht-university rcsb

metaspace

Cloud engine and platform for metabolite annotation for imaging mass spectrometry

✭ 36

typescript python Vue javascript SCSS shell cloud bioinformatics metabolomics

PHIST

Phage-Host Interaction Search Tool

✭ 19

C++python Makefile bioinformatics genomics bacterial-genomes k-mers phages host-prediction

rna-seq-snakemake

Snakemake based pipeline for RNA-Seq analysis

✭ 29

r python PowerBuilder shell bioinformatics snakemake pipeline rna-seq-analysis rna-seq-snakemake

libBigWig

A C library for handling bigWig files

✭ 61

c python CMake Makefile bioinformatics bigwig bigbed

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