Topic: bioinformatics-scripts Goto Github

👇 Here are 164 public repositories matching this topic...

alvesrco / pipecov
bioinformatics-scripts,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).
User: alvesrco
covid19 genomics bioinformatics-pipeline bioinformatics-analysis bioinformatics-scripts

amojarro / carrierseq
bioinformatics-scripts,a sequence analysis workflow for low-input nanopore sequencing
User: amojarro
nanopore bioinformatics-scripts metagenomics docker

anand84471 / pythonforbioinformatics
bioinformatics-scripts,This repository will be helpful to start using python for your Bioinformatics projects.
User: anand84471
Home Page: https://readmycourse.com
python bioinfomatics bioinformatics-scripts

arendsee / bioinfo-utils
bioinformatics-scripts,A gallimaufry of questionable shellscripts
User: arendsee
bioinformatics-scripts scripts-collection bioinformatics

brianyiktaktsui / skymap
bioinformatics-scripts,High-throughput gene to knowledge mapping through massive integration of public sequencing data.
User: brianyiktaktsui
Home Page: https://github.com/brianyiktaktsui/Skymap/blob/master/README.md
bioinformatics-pipeline bioinformatics-analysis bioinformatics-scripts big-data

bystrogenomics / bystro
bioinformatics-scripts,Bystro genetic analysis (annotation, filtering, statistics)
Organization: bystrogenomics
bioinformatics bioinformatics-algorithms bioinformatics-analysis bioinformatics-databases bioinformatics-pipeline bioinformatics-scripts genomics genomics-search

cbp44 / samflags
bioinformatics-scripts,Command line utility written in NodeJS to decode SAM flags to explain what they mean.
User: cbp44
samtools sam bam bioinformatics bioinformatics-scripts sam-bam sam-flags

danangcrysnanto / bovine-graphs-mapping
bioinformatics-scripts,Comparison of sequencing read mapping to pangenome graphs
User: danangcrysnanto
genomic bioinformatics bioinformatics-scripts graphs bioinformatics-pipeline

dvklopfenstein / reactomepy
bioinformatics-scripts,Explore biomolecular pathways in Reactome from the command-line or a Python script
User: dvklopfenstein
reactome reactome-pathway biological-networks molecular-biology pathway-enrichment-analysis pathway-analysis biotechnology biotech bioinformatics bioinformatics-pipeline bioinformatics-analysis bioinformatics-scripts bioinformatics-tool pathway-models protein-protein-interaction

emmawahl / facepai
bioinformatics-scripts,Scripts for executing a filtering, clustering and identification pipeline for eDNA samples.
User: emmawahl
bioinformatics bioinformatics-pipeline bioinformatics-scripts biology dna-barcode dna-sequences environmental-dna molecular-biology

fabianjetzinger / sort_gtf
bioinformatics-scripts,Shell script to sort .gtf files
User: fabianjetzinger
bioinformatics bioinformatics-data bioinformatics-scripts

fallerlab / ribo-oddr
bioinformatics-scripts,Ribo-seq focused Oligo Design pipeline for experiment-specific Depletion of Ribosomal RNAs
User: fallerlab
rrna ribosome-profiling riboseq rna-seq oligo-design bioinformatics bioinformatics-pipeline computational-biology bioinformatics-scripts bioinformatics-tool

fg6 / yeaststrainsstudy
bioinformatics-scripts,Scripts to download the PacBio, ONT and MiSeq datasets used in https://www.nature.com/articles/s41598-017-03996-z and run the pipelines as described in the paper or simply download the final assemblies as generated by the authors.
User: fg6
oxford-nanopore pacbio miseq pipelines yeast bioinformatics-scripts bioinformatics-data

flystar233 / pyscript-bio
bioinformatics-scripts,生物信息学python代码，专注于重测序文本计算、处理
User: flystar233
bioinformatics-scripts python3

fomightez / blast-binder
bioinformatics-scripts,Repo for running command line-based BLAST in Jupyter environment provided via Binder.
User: fomightez
python genomics protein-sequences dna rna pandas pandas-dataframe bioinformatics-analysis bioinformatics bioinformatics-scripts

fomightez / pdbepisa-binder
bioinformatics-scripts,Using data from PDBePISA with the convenience of Python and Jupyter.
User: fomightez
python bioinformatics snakemake genomics protein-structure pandas bioinformatics-pipeline protein-sequences bioinformatics-analysis nucleic-acids

fomightez / sequencework
bioinformatics-scripts,programs and scripts, mainly python, for analyses related to nucleic or protein sequences
User: fomightez
python genomics protein-sequences dna rna lists list bioinformatics-analysis bioinformatics-scripts bioinformatics

gkoulouras / seq-sec-ratio
bioinformatics-scripts,A console application for the estimation of the primary and secondary structure's elements. Input should be the FASTA-formatted "ss.txt" file generated by PDB database.
User: gkoulouras
Home Page: http://apps.grigoriskoulouras.com/software/seqsecanalyzer_ver_1.0.zip
pdb pdb-files ss-txt amino-acids secondary-structure bioinformatics-data bioinformatics-scripts bioinformatics-databases vb-net protein-data-bank

huffordlab / nam-genomes
bioinformatics-scripts,Detailed bioinformatics scripts and methods used in the NAM genome paper.
Organization: huffordlab
Home Page: https://nam-genomes.org
bioinformatics-analysis bioinformatics-scripts genome-assembly genomics maize nam

jfresnedo / ampseq
bioinformatics-scripts,A framework for semi-automated analysis of Amplicon Sequencing data
User: jfresnedo
bioinformatics bioinformatics-pipeline bioinformatics-scripts bioinformatics-containers bioinformatics-data singularity-containers singularity-hub

johnnytam100 / pdb2uniprot
bioinformatics-scripts,A Python script to map PDB ID + chain ID to UniProt ID.
User: johnnytam100
bioinformatics bioinformatics-scripts bioinformatics-tool mapping pdb-database pdb-files pdb-structure rcsb uniprot uniprot-ids uniprotkb

lazappi / binf-scripts
bioinformatics-scripts,A collection of useful bioinformatics scripts.
User: lazappi
bioinformatics bioinformatics-scripts

mauriceling / bactome
bioinformatics-scripts,Toolbox for Studying Bacteria, Archaea, and Complex Taxons
User: mauriceling
Home Page: https://github.com/mauriceling/bactome/wiki
python bioinformatics bioinformatics-scripts statistical-genetics genome-analysis proteomics

minesh1291 / howtobioinformatics
bioinformatics-scripts,:man_scientist: Analysis Pipelines and Useful Tools
User: minesh1291
Home Page: https://github.com/minesh1291/HowToBioinformatics
bioinformatics-pipeline bioinformatics-analysis bioinformatics-scripts

mughal41 / automate_hetatm_removal
bioinformatics-scripts,Script to Automate removal of HETATOMS
User: mughal41
automation bioinformatics-scripts pdb python

nmtrang00 / var_annot_eval
bioinformatics-scripts,An empirical variant annotation and data evaluation pipeline.
User: nmtrang00
bioinformatics-pipeline bioinformatics bioinformatics-analysis bioinformatics-scripts bioinformatics-tool variant-annotations data-evaluation data-analysis

orangesi / pykits
bioinformatics-scripts,simple python script for bioinformatics
User: orangesi
python3 pandas-python fire-python biopython bioinformatics-scripts fasta

orionzhou / maize
bioinformatics-scripts,bioinformatic utility libraries in python
User: orionzhou
bioinformatics bioinformatics-pipeline bioinformatics-scripts maize python

parisepigenetics / rna_feat_ext
bioinformatics-scripts,Software tools to extract mRNA's features from a list of ENSEMBL gene IDs.
Organization: parisepigenetics
Home Page: https://parisepigenetics.github.io/rna_feat_ext/
bioinformatics bioinformatics-scripts

peterk87 / filter_classified_reads
bioinformatics-scripts,Filter for reads from taxa of interest using Kraken2/Centrifuge classification results.
User: peterk87
taxonomic-classification dna-sequences bioinformatics-scripts filtering

platonb / bioinformatic-python-scripts
bioinformatics-scripts,Простые биоинформатические скрипты на Python 3. Удобная и гибкая замена Excel/Calc для решения повседневных рутинных задач вычислительной биологии.
User: platonb
bioinformatics bioinformatics-pipeline bioinformatics-scripts bioinformatics-algorithms bioinformatic-tools python3 opensource vigg

pollytikhonova / imgqfinder
bioinformatics-scripts,The official python version of ImGQfinder: http://imgqfinder.niifhm.ru/ A tool that finds gquadruplexes and imotifs.
User: pollytikhonova
bioinformatics bioinformatics-scripts bioinformatics-tool quadruplexes g-quadruplexes imotifs dna

pwwang / biopipen
bioinformatics-scripts,A set of processes/pipelines for bioinformatics
User: pwwang
Home Page: https://pwwang.github.io/biopipen
bioinformatics bioinformatics-pipeline bioinformatics-scripts pipeline-framework

ramsainanduri / split_multi_fasta
bioinformatics-scripts,Split multi fasta file into single fasta files
User: ramsainanduri
bioinformatics-scripts bioinformatics bioinformatics-tool fasta-sequences

robinvanderlee / positive-selection
bioinformatics-scripts,Scripts and procedures for detecting positively selected genes and codons in primates
User: robinvanderlee
Home Page: https://doi.org/10.1093/nar/gkx704
bioinformatics bioinformatics-pipeline bioinformatics-scripts bioinformatics-analysis computational-biology evolution comparative-genomics positive-selection primates genetics

samilhll / rbhxpress
bioinformatics-scripts,A shell script that uses diamond to compute the reciprocal best hits between two proteomes in a rush.
User: samilhll
bioinformatics-scripts orthology-inference

seb943 / smith_waterman_py
bioinformatics-scripts,Implementing the Smith-Waterman algorithm in Python
User: seb943
bioinformatics bioinformatics-scripts bioinformatics-tool dynamic-programming python smith-waterman smith-waterman-algorithm

southgreenplatform / gemo
bioinformatics-scripts,A mosaic genome painting tool for plant genomes
Organization: southgreenplatform
Home Page: https://gemo.readthedocs.io/en/latest/index.html
bioinformatics bioinformatics-scripts genomes karyotype plants visualization web

surh / pbi
bioinformatics-scripts,Microbiome analysis for phosphate-defense interaction
User: surh
microbiome microbiome-analysis plants bioinformatics-scripts bioinformatics-analysis plant-pathology plant-immunity phosphorus

sydney-informatics-hub / bioinformatics
bioinformatics-scripts,A suite of bioinformatics data processing and analysis pipelines, software, and training resources for common DNA and RNA sequence analysis methods.
Organization: sydney-informatics-hub
bioinformatics bioinformatics-pipeline bioinformatics-scripts bioinformatics-analysis sydney-informatics-hub research-computing germline-variants somatic-variants cancer genomics

tgolubch / castanet
bioinformatics-scripts,Data processing scripts for analysis of targeted metagenomics sequencing data. Intended for use with multiplexed Illumina short-read data generated after enrichment.
User: tgolubch
metagenomics python bash bioinformatics-scripts bioinformatics pathogenomics pathogen viruses bacteria enrichment

tomarovsky / biocrutch
bioinformatics-scripts,Various bioinformatics scripts
User: tomarovsky
bioinformatics bioinformatics-scripts

ulelab / peka
bioinformatics-scripts,Find motifs enriched around prominent crosslinks
Organization: ulelab
bioinformatics bioinformatics-analysis bioinformatics-scripts

v-z / hybseq-scripts
bioinformatics-scripts,Set of scripts to process HybSeq target enrichment HTS data (on computing grids).
User: v-z
Home Page: https://github.com/V-Z/hybseq-scripts
alignments bioinformatics bioinformatics-analysis bioinformatics-pipeline bioinformatics-scripts data-analysis data-science gene-tree genomics hybpiper hybseq-data hybseq-scripts metacentrum molecular-biology ngs ngs-pipeline ngs-scripts paralogs phylogenomics species-tree

vimalkvn / riboplot
bioinformatics-scripts,RiboPlot includes programs to plot and output Ribo-Seq read counts from an alignment file (BAM format).
User: vimalkvn
ngs ribosome-profiling riboseq bioinformatics bioinformatics-scripts

vinuesa / tib-filoinfo
bioinformatics-scripts,Talleres Internacionales de Bioinformática - Centro de Ciencias Genómicas, UNAM, Cuernavaca, México
User: vinuesa
bash-scripting bioinformatics-scripts blast linux-shell maximum-likelihood model-selection multiple-sequence-alignment phylogenetics reciprocal-blast-hits tutorials

widdowquinn / find_differential_primers
bioinformatics-scripts,Code for design of diagnostic PCR primers, and metabarcoding markers.
User: widdowquinn
Home Page: https://widdowquinn.github.io/find_differential_primers/
bioinformatics bioinformatics-scripts primer-design qpcr diagnostics diagnostic-primers

zd200572 / bioinfor-python
bioinformatics-scripts,bioinformatics
User: zd200572
bioinformatics-scripts python3

zealousgeneticist / cartoflow
bioinformatics-scripts,A Python workflow for taking chemicals, finding the genes they interact with, and mapping the communities of genetic interactions.
User: zealousgeneticist
api bioinformatics bioinformatics-analysis bioinformatics-databases bioinformatics-pipeline bioinformatics-scripts bioinformatics-tool bioinformatics-visualization

zhangsjsky / cstk
bioinformatics-scripts,C & S's Toolkit
User: zhangsjsky
data-visualization bioinformatics bioinformatics-scripts statistics-toolbox figure-maker