bioinformatics-scripts

There are 36 repositories under bioinformatics-scripts topic.

HuffordLab / NAM-genomes
Detailed bioinformatics scripts and methods used in the NAM genome paper.
bioinformatics-analysis maize genome-assembly genomics bioinformatics-scripts nam
Language:R 85
widdowquinn / find_differential_primers
Code for design of diagnostic PCR primers, and metabarcoding markers.
bioinformatics bioinformatics-scripts diagnostic-primers diagnostics primer-design qpcr
Language:Python 63
bystrogenomics / bystro
Natural Language Search and Analysis of High Dimensional Genomic Data
genomics genomics-search bioinformatics bioinformatics-pipeline bioinformatics-analysis bioinformatics-databases bioinformatics-algorithms bioinformatics-scripts
Language:Python 48
brianyiktaktsui / Skymap
High-throughput gene to knowledge mapping through massive integration of public sequencing data.
bioinformatics-pipeline bioinformatics-analysis bioinformatics-scripts big-data
Language:Jupyter Notebook 31
flystar233 / pyscript-bio
生物信息学python代码，专注于重测序文本计算、处理
python3 bioinformatics-scripts
Language:Python 27
vinuesa / TIB-filoinfo
Talleres Internacionales de Bioinformática - Centro de Ciencias Genómicas, UNAM, Cuernavaca, México
bash-scripting bioinformatics-scripts blast linux-shell maximum-likelihood model-selection multiple-sequence-alignment phylogenetics reciprocal-blast-hits tutorials bioinformatics pangenomics phylogenomics hmmer3 profile-hmms
Language:Shell 26
dvklopfenstein / ReactomePy
Explore biomolecular pathways in Reactome from the command-line or a Python script
bioinformatics bioinformatics-analysis bioinformatics-pipeline bioinformatics-scripts bioinformatics-tool biological-networks biotech biotechnology molecular-biology pathway-analysis pathway-enrichment-analysis pathway-models protein-protein-interaction reactome reactome-pathway
Language:Python 24
sequencework
fomightez / sequencework
programs and scripts, mainly python, for analyses related to nucleic or protein sequences
python genomics protein-sequences dna rna lists list bioinformatics-analysis bioinformatics-scripts bioinformatics
Language:Python 24
robinvanderlee / positive-selection
Scripts and procedures for detecting positively selected genes and codons in primates
bioinformatics bioinformatics-pipeline bioinformatics-scripts bioinformatics-analysis computational-biology evolution comparative-genomics positive-selection primates genetics sequence-alignment genomics genomes genome-analysis codeml immunity ensembl
Language:Perl 21
johnnytam100 / pdb2uniprot
A Python script to map PDB ID + chain ID to UniProt ID.
bioinformatics bioinformatics-scripts bioinformatics-tool mapping pdb-database pdb-files pdb-structure rcsb uniprot uniprot-ids uniprotkb
Language:Python 17
SouthGreenPlatform / GeMo
A mosaic genome painting tool for plant genomes
bioinformatics bioinformatics-scripts genomes karyotype plants visualization web
Language:JavaScript 17
Sydney-Informatics-Hub / Bioinformatics
A suite of bioinformatics data processing and analysis pipelines, software, and training resources for common methods.
bioinformatics bioinformatics-pipeline bioinformatics-scripts bioinformatics-analysis sydney-informatics-hub research-computing germline-variants somatic-variants cancer genomics indels metagenomics ngs rnaseq snps transcriptomics variant-calling nextflow nextflow-pipelines
17
alvesrco / pipecov
This project proposes to contribute to fill the knowledge gap about Covid-19SARS-CoV-2 in Brazil and with the global knowledge about the pathogen. The scientific community and governments of other countries are looking for actions along these lines. The United Kingdom recently established a research network for genomic studies of SARS-CoV-2Covid-19 with a contribution of GBP 20 million (https://www.gov.uk/government/news/uk-launches-whole- genome-sequence-alliance-to-map-spread-of-coronavirus).
covid19 genomics bioinformatics-pipeline bioinformatics-analysis bioinformatics-scripts
Language:R 14
pwwang / biopipen
A set of processes/pipelines for bioinformatics
bioinformatics bioinformatics-pipeline bioinformatics-scripts pipeline-framework
Language:Python 13
ramsainanduri / split_multi_fasta
Split multi fasta file into single fasta files
bioinformatics-scripts bioinformatics bioinformatics-tool fasta-sequences
Language:Python 9
lazappi / binf-scripts
A collection of useful bioinformatics scripts.
bioinformatics bioinformatics-scripts
Language:Python 8
minesh1291 / HowToBioinformatics
:man_scientist: Analysis Pipelines and Useful Tools
bioinformatics-pipeline bioinformatics-analysis bioinformatics-scripts
Language:R 8
tomarovsky / Biocrutch
Various bioinformatics scripts
bioinformatics bioinformatics-scripts
Language:Python 8
fomightez / blast-binder
Repo for running command line-based BLAST in Jupyter environment provided via Binder.
python genomics protein-sequences dna rna pandas pandas-dataframe bioinformatics-analysis bioinformatics bioinformatics-scripts
Language:Jupyter Notebook 7
fomightez / pdbepisa-binder
Using data from PDBePISA with the convenience of Python and Jupyter.
python bioinformatics snakemake genomics protein-structure pandas bioinformatics-pipeline protein-sequences bioinformatics-analysis nucleic-acids nucleic-sequence bioinformatics-scripts pandas-dataframe
Language:Jupyter Notebook 7
peterk87 / filter_classified_reads
Filter for reads from taxa of interest using Kraken2/Centrifuge classification results.
taxonomic-classification dna-sequences bioinformatics-scripts filtering
Language:Python 7
amojarro / carrierseq
a sequence analysis workflow for low-input nanopore sequencing
nanopore bioinformatics-scripts metagenomics docker
Language:Shell 6
danangcrysnanto / bovine-graphs-mapping
Comparison of sequencing read mapping to pangenome graphs
bioinformatics bioinformatics-pipeline bioinformatics-scripts genomic graphs
Language:Jupyter Notebook 6
facepai
emmawahl / facepai
Scripts for executing a filtering, clustering and identification pipeline for eDNA samples.
bioinformatics bioinformatics-pipeline bioinformatics-scripts biology molecular-biology dna-sequences dna-barcode environmental-dna
Language:Shell 6
PlatonB / bioinformatic-python-scripts
Простые биоинформатические скрипты на Python 3. Удобная и гибкая замена Excel/Calc для решения повседневных рутинных задач вычислительной биологии.
bioinformatic-tools bioinformatics bioinformatics-algorithms bioinformatics-pipeline bioinformatics-scripts opensource python3 vigg
Language:Python 6
ulelab / peka
Find motifs enriched around prominent crosslinks
bioinformatics bioinformatics-analysis bioinformatics-scripts
Language:Python 6
fallerlab / Ribo-ODDR
Ribo-seq focused Oligo Design pipeline for experiment-specific Depletion of Ribosomal RNAs
rrna ribosome-profiling riboseq rna-seq oligo-design bioinformatics bioinformatics-pipeline computational-biology bioinformatics-scripts bioinformatics-tool oligonucleotide
Language:Python 5
mauriceling / bactome
Toolbox for Studying Bacteria, Archaea, and Complex Taxons
python bioinformatics bioinformatics-scripts statistical-genetics genome-analysis proteomics
Language:HTML 5
orionzhou / maize
bioinformatic utility libraries in python
bioinformatics bioinformatics-pipeline bioinformatics-scripts maize python
Language:Python 5
rbhXpress
SamiLhll / rbhXpress
A shell script that uses diamond to compute the reciprocal best hits between two proteomes in a rush.
bioinformatics-scripts orthology-inference
Language:Shell 5
anand84471 / PythonForBioinformatics
This repository will be helpful to start using python for your Bioinformatics projects.
python bioinfomatics bioinformatics-scripts
Language:Python 4
cbp44 / samflags
Command line utility written in NodeJS to decode SAM flags to explain what they mean.
bam bioinformatics bioinformatics-scripts sam sam-bam sam-flags samtools
Language:JavaScript 4
gibbslab / biobash
Common BASH routines for computational biology
bioinformatics-analysis bioinformatics bioinformatics-tool bioinformatics-scripts bash bash-scripting genomic-data-analysis transcriptomics
Language:Shell 4
PollyTikhonova / ImGQfinder
The official python version of ImGQfinder: http://imgqfinder.niifhm.ru/ A tool that finds gquadruplexes and imotifs.
bioinformatics bioinformatics-scripts bioinformatics-tool dna g-quadruplexes imotifs quadruplexes
Language:Python 4
roseedwin / Benchmarking-taxonomic-classifiers-for-soil-shotgun-data
Benchmarking various taxonomic classifiers for profiling soil metagenomic data, with scripts and tools tailored for fungal, bacterial, and archaeal genome identification.
benchmarking bioinformatics-analysis bioinformatics-scripts gtdb kaiju kraken metaphlan taxonomic-classification soil-metagenomics
Language:R 4
V-Z / hybseq-scripts
Set of scripts to process HybSeq target enrichment HTS data (on computing grids).
ngs-pipeline hybseq-data phylogenomics ngs data-science data-analysis molecular-biology paralogs bioinformatics-pipeline bioinformatics-scripts bioinformatics-analysis genomics bioinformatics hybpiper gene-tree alignments species-tree hybseq-scripts metacentrum ngs-scripts
Language:Shell 4