PollyTikhonova/ImGQfinder

The official python version of ImGQfinder: http://imgqfinder.niifhm.ru/ A tool that finds gquadruplexes and imotifs.

Language: Python - Size: 235 KB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 4 - Forks: 0

ulelab/bs_assign

Find groups of motifs around genomic landmarks of interest

Language: Python - Size: 34.2 KB - Last synced at: 3 months ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

shiqijialab/insm1thymus

Data analysis code

Language: Jupyter Notebook - Size: 1.91 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 1

wushyer/One-line-command-for-bioinformatics

Language: Awk - Size: 5.86 KB - Last synced at: almost 2 years ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 0

zd200572/bioinfor-python

bioinformatics

Language: Python - Size: 217 KB - Last synced at: almost 2 years ago - Pushed at: over 7 years ago - Stars: 2 - Forks: 2

loggy01/EBV-transcript-variation-pipeline

Calculates Cp- and Wp-initiated transcript variation (Epstein-Barr virus)

Language: R - Size: 950 KB - Last synced at: almost 2 years ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0

fatmakahveci/milestone

bacterial strain identification

Language: Python - Size: 8.78 MB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

sagarnikam123/bioinfoProject

a project for fulfillment of M.Sc in Bioinformatics

Language: R - Size: 503 KB - Last synced at: almost 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

brianyiktaktsui/Skymap

High-throughput gene to knowledge mapping through massive integration of public sequencing data.

Language: Jupyter Notebook - Size: 23.7 MB - Last synced at: almost 2 years ago - Pushed at: over 6 years ago - Stars: 31 - Forks: 3

renatawong/bioinformatics-algorithms

Python implementation of bioinformatics algorithms and useful functions.

Language: Python - Size: 4.53 MB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0

mauriceling/bactome

Toolbox for Studying Bacteria, Archaea, and Complex Taxons

Language: HTML - Size: 10.4 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 5 - Forks: 55

V-Z/structure-multi-pbspro

Set of scripts to run STRUCTURE in parallel on computing grids like MetaCentrum. Scripts are designed for grids and clusters using PBS Pro, but can be easily adopted for another queue system.

Language: Shell - Size: 83 KB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 1

mr-y/my_bioinfPerls

Perl scripts for bioinformatics

Language: Perl - Size: 38.1 KB - Last synced at: almost 2 years ago - Pushed at: almost 4 years ago - Stars: 1 - Forks: 1

PlatonB/bioinformatic-python-scripts

Простые биоинформатические скрипты на Python 3. Удобная и гибкая замена Excel/Calc для решения повседневных рутинных задач вычислительной биологии.

Language: Python - Size: 299 KB - Last synced at: 5 days ago - Pushed at: over 5 years ago - Stars: 6 - Forks: 3

sablokgaurav/plant_single_cell_RNA_analysis

single_cell_RNA_analysis

Size: 1000 Bytes - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0

fomightez/blast-binder

Repo for running command line-based BLAST in Jupyter environment provided via Binder.

Language: Jupyter Notebook - Size: 2.06 MB - Last synced at: 3 months ago - Pushed at: over 1 year ago - Stars: 7 - Forks: 5

SamiLhll/OF_to_macrosyntR

Shell script to post-process OrthoFinder's output into pairwise tables used in macrosyntR

Language: Shell - Size: 25.4 KB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

kc-moharana/bioinformatics_codes

My PERL and other UNIX based codes developed while analysing NGS, microarray other data.

Language: Perl - Size: 612 KB - Last synced at: over 2 years ago - Pushed at: over 6 years ago - Stars: 2 - Forks: 2

gkoulouras/seq-sec-ratio

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.

Language: Visual Basic - Size: 812 KB - Last synced at: over 1 year ago - Pushed at: about 6 years ago - Stars: 3 - Forks: 0

avle98/MQP20

WPI Bioinformatics/Computational Major Qualifying Project 2019-2020

Language: Rich Text Format - Size: 31.6 MB - Last synced at: over 2 years ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 0

anand84471/PythonForBioinformatics

This repository will be helpful to start using python for your Bioinformatics projects.

Language: Python - Size: 723 KB - Last synced at: over 2 years ago - Pushed at: about 4 years ago - Stars: 3 - Forks: 3

orionzhou/maize 📦

bioinformatic utility libraries in python

Language: Python - Size: 998 KB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 5 - Forks: 2

SamiLhll/rbhXpress

A shell script that uses diamond to compute the reciprocal best hits between two proteomes in a rush.

Language: Shell - Size: 12.3 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 0

peterk87/filter_classified_reads

Filter for reads from taxa of interest using Kraken2/Centrifuge classification results.

Language: Python - Size: 1.53 MB - Last synced at: 19 days ago - Pushed at: over 2 years ago - Stars: 7 - Forks: 1

mateuszstompor/Rosalind

Contains solutions to problems posted on rosalind.info

Language: Python - Size: 1.44 MB - Last synced at: over 2 years ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0

ElRakabawi/cgr-perl

chaos game representation for DNA seqs in Perl.

Language: Perl - Size: 13.7 KB - Last synced at: about 1 year ago - Pushed at: about 7 years ago - Stars: 1 - Forks: 0

gibbslab/biobash Fork of ampinzonv/biobash

Common BASH routines for computational biology

Language: Shell - Size: 17.6 MB - Last synced at: over 2 years ago - Pushed at: about 3 years ago - Stars: 2 - Forks: 3

dabane-ghassan/GFF-GTF-analysis

A bioinformatics script to analyse GFF/GTF files

Language: Python - Size: 8.79 KB - Last synced at: over 2 years ago - Pushed at: almost 5 years ago - Stars: 1 - Forks: 0

imengyuan/Bioinfo-pipelines

Sample bioinfo script collection.

Language: Python - Size: 29.9 MB - Last synced at: over 2 years ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 2

amojarro/carrierseq

a sequence analysis workflow for low-input nanopore sequencing

Language: Shell - Size: 1.61 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 6 - Forks: 1

bhaveshashok/AutoDockVina-BatchSubmission

A simple batch submission script to submit jobs to AutoDock Vina on Linux and MacOS developed by Bhavesh Ashok.

Language: Shell - Size: 16.6 KB - Last synced at: over 2 years ago - Pushed at: almost 5 years ago - Stars: 1 - Forks: 1

V-Z/RAD-Seq-scripts

Set of scripts to process RAD-Seq HTS data on computing grids like MetaCentrum.

Language: Shell - Size: 5.14 MB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0

jithin8mathew/Bioinformatics

Python scripts for Bioinformatics applications

Language: Python - Size: 60.5 MB - Last synced at: over 2 years ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 0

orangeSi/pykits

simple python script for bioinformatics

Language: Python - Size: 83 KB - Last synced at: 4 months ago - Pushed at: about 6 years ago - Stars: 2 - Forks: 0

annkamsk/motif-analysis

Simple bioinf pipeline incl. related sequences search, identifying regulatory regions and motifs, and enrichment analysis.

Language: Python - Size: 914 KB - Last synced at: over 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

nmtrang00/Var_Annot_Eval

An empirical variant annotation and data evaluation pipeline.

Language: Python - Size: 43 KB - Last synced at: over 2 years ago - Pushed at: over 3 years ago - Stars: 3 - Forks: 1

Amirreza-Mousavi/R_Meets_Uniprot

A short script for searching in Uniprot using RESTful APIs

Language: R - Size: 196 KB - Last synced at: 9 months ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

Atif2227/Bioinformaticts-with-Python

This repository has some basic bioinformatics activity/operations done in Python. Although, there are n number of offline and online tools doing these jobs but still, doing these jobs by own coding would give you a proper insight into how those available tools work at the coding level. Don't just copy the codes, rather try to understand the logic behind it and more importantly try to make these codes even better.

Language: Jupyter Notebook - Size: 267 KB - Last synced at: 7 months ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

fomightez/hhsuite3-binder

Repo for running command line-based HH-suite3 software in Jupyter environment provided via Binder.

Language: Jupyter Notebook - Size: 590 KB - Last synced at: about 1 month ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 1

joaomota59/bioInformatica

Programas usados em BioInformática

Language: Jupyter Notebook - Size: 1.77 MB - Last synced at: over 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

PowersPope/Deduper-PowersPope

Tool to remove PCR duplicates

Language: HTML - Size: 3.56 MB - Last synced at: over 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

svsuresh/rscripts

Repository miscellaneous R scripts including scripts for RNAseq analysis

Language: Jupyter Notebook - Size: 1.95 MB - Last synced at: almost 2 years ago - Pushed at: almost 4 years ago - Stars: 2 - Forks: 0

ada5tra/bioinformatics

Bioinformatics projects and linux scripts.

Language: Shell - Size: 9.43 MB - Last synced at: 6 months ago - Pushed at: about 4 years ago - Stars: 0 - Forks: 1

EricHugo/bioUtils

Language: Python - Size: 33.2 KB - Last synced at: about 2 years ago - Pushed at: about 4 years ago - Stars: 1 - Forks: 0

MillironX/sc2-sequencing

File manipulation/bioinformatics-type scripts that my colleagues have found useful in sequencing SARS-CoV2 (SC2).

Language: Julia - Size: 80.1 KB - Last synced at: 3 months ago - Pushed at: about 4 years ago - Stars: 0 - Forks: 0

Matthew-Mosior/Fasta-Region-Randomizer

A Haskell script for creating random single nucleotide variants within genomic region(s) using a genomic window string.

Language: Haskell - Size: 26.8 MB - Last synced at: 10 days ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

dabane-ghassan/ProjetM1S1Bioinfo

First semester bioinformatics project

Language: Python - Size: 70.2 MB - Last synced at: over 2 years ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 1

Matthew-Mosior/Basic-Variant-Selector

A Haskell script for selecting variants from a variant calling format (vcf) file based on variants present in a mgibed file.

Language: Haskell - Size: 1.83 MB - Last synced at: 10 days ago - Pushed at: about 6 years ago - Stars: 0 - Forks: 0

ainefairbrother/GenBank-parser

This is a parser written to extract data from a GenBank file and insert it into an SQL database. This is part of a project that I did for my MSc in Bioinformatics.

Language: Python - Size: 12.7 KB - Last synced at: over 2 years ago - Pushed at: almost 7 years ago - Stars: 1 - Forks: 0

LuisSoares/Manuscript

Scripts used to created manuscript figures

Language: Jupyter Notebook - Size: 6.28 MB - Last synced at: 3 months ago - Pushed at: over 8 years ago - Stars: 1 - Forks: 0

avera1988/Comparative_genomics

Toolbox for comparative genomics

Language: Shell - Size: 58.6 KB - Last synced at: almost 2 years ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 1

Matthew-Mosior/Representative-Sample-Chooser

A Haskell script that performs hierarchical filtering on a tab-delimited file across groups of lines based on user-defined hierarchical filtering string.

Language: Haskell - Size: 3 MB - Last synced at: 10 days ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 0

tdayris/yawn

A bunch of scripts for actions I have to do on a regular basis

Language: Python - Size: 158 KB - Last synced at: about 2 years ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0

surh/pbi

Microbiome analysis for phosphate-defense interaction

Language: R - Size: 149 KB - Last synced at: over 2 years ago - Pushed at: over 5 years ago - Stars: 4 - Forks: 2

shizhuoxing/Full-Length-RNA-Toolkit

Useful tools for Full-Length RNA analysis.

Size: 17.6 KB - Last synced at: about 2 years ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 1

Matthew-Mosior/HuMo-Create-Variant-File

A Haskell script that creates a master variant file given sample information and variant information.

Language: Haskell - Size: 1.31 MB - Last synced at: 10 days ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0

Matthew-Mosior/Variant-to-bam-readcount

A Haskell script for creating input files for bam-readcount from ensembl-vep output and variant-calling format (vcf) files.

Language: Haskell - Size: 3.41 MB - Last synced at: 10 days ago - Pushed at: almost 6 years ago - Stars: 0 - Forks: 1

matteodelucchi/TR_CNV_in_expression_data

Pipeline to prepare RNA sequencing data for tandem repeat annotation with TRAL

Language: Shell - Size: 1.01 MB - Last synced at: 4 months ago - Pushed at: almost 6 years ago - Stars: 0 - Forks: 0

bixBeta/xcode.beta

SLURM job temps @UALBANY

Language: Shell - Size: 14.6 KB - Last synced at: over 2 years ago - Pushed at: about 7 years ago - Stars: 1 - Forks: 0

PsiPhiTheta/Bioinformatics-Labs

Genome analysis scripts and laboratory files for the UofT Bioinformatics course

Language: R - Size: 7.79 MB - Last synced at: over 2 years ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 0

hexhead/Rinbix

R package implementations and interfaces to In silico research group's bioinformatics toolbox inbix

Language: R - Size: 652 KB - Last synced at: over 2 years ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 0

jeffreypullin/myCyTOF

Functions and scripts for analysing and normalising CyTOF data

Language: HTML - Size: 416 MB - Last synced at: 3 months ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 1

kevinxchan/bioinfotools

Various scripts for bioinformatic purposes.

Language: Python - Size: 13.7 KB - Last synced at: over 2 years ago - Pushed at: almost 7 years ago - Stars: 0 - Forks: 0

hassanfa/GFFtoolkit

Extracts information from GFF and prepare them in bed format

Language: Shell - Size: 1.06 MB - Last synced at: over 2 years ago - Pushed at: almost 7 years ago - Stars: 0 - Forks: 1

carrineblank/MicroPIEDigester

Converts raw phenotypic character information generated by MicroPIE into a coded character matrix (nexus file).

Language: Perl - Size: 1.23 MB - Last synced at: over 2 years ago - Pushed at: about 7 years ago - Stars: 0 - Forks: 0

mbhall88/tinysink

Synchronise Nanopore reads with a server.

Language: Shell - Size: 8.79 KB - Last synced at: 5 days ago - Pushed at: about 7 years ago - Stars: 1 - Forks: 1

Bio-designer/bioinfo-scripts

Language: Python - Size: 1000 Bytes - Last synced at: over 2 years ago - Pushed at: about 7 years ago - Stars: 0 - Forks: 0

neuhofmo/count_gaps_in_fasta

A script which counts the gaps in FASTA DNA sequences and reports their proportions in a CSV file

Language: Python - Size: 1.95 KB - Last synced at: over 2 years ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 0

Santi-7/DNA_conservation_index

This program calculates the conservation index of a set of DNA or protein sequences

Language: Python - Size: 16.6 KB - Last synced at: over 2 years ago - Pushed at: about 8 years ago - Stars: 0 - Forks: 0

Bohdan-Khomtchouk/Differential-expression-scripts

Miscellaneous differential gene expression scripts in R

Language: R - Size: 1.95 KB - Last synced at: over 2 years ago - Pushed at: about 9 years ago - Stars: 1 - Forks: 0

elwlwlwk/GeneSeq2Taxonomy

Taxonomy Classifer Using Gene Sequence.

Language: Python - Size: 20.5 KB - Last synced at: over 2 years ago - Pushed at: almost 8 years ago - Stars: 0 - Forks: 0