GitHub topics: ngs-analysis

Repositories

CCBR/CHARLIE

Circrnas in Host And viRuses anaLysis pIpEline for Detection Annotation Quantification of circRNAs

Language: Python - Size: 278 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 2 - Forks: 2

gabrielvpina/bioinfo_scripts

some scripts used in bioinformatics research

Language: Shell - Size: 11.4 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 1 - Forks: 0

sib-swiss/sequencing-data-analysis-training

SIB course that introduces analysis of NGS data

Language: Shell - Size: 53.2 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 16 - Forks: 13

meeranhussain/Population_genomic_analysis

A repository for efficient population genomic analysis using Snakemake workflow.

Language: R - Size: 919 KB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 0 - Forks: 0

gabrielvpina/viralquest

A pipeline for viral diversity analysis

Language: Python - Size: 49.7 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 0 - Forks: 0

PavlidisLab/rnaseq-pipeline

RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.

Language: Shell - Size: 43.5 MB - Last synced at: 10 days ago - Pushed at: 11 days ago - Stars: 24 - Forks: 5

adnantariq6400/Identification-of-key-taxonomic-and-metabolic-players

Metagenome Project

Language: Shell - Size: 7.81 KB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 0 - Forks: 0

jdieramon/master_biotec_NGS

Análisis genómicos y transcriptómicos con plataforma NGS

Language: HTML - Size: 6.68 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 0 - Forks: 0

ratope/VariantFilteringCriteriaVvTempranillo

List of the filtering criteria of the variants called in samples of Vitis vinifera cv. Tempranillo

Size: 85.9 KB - Last synced at: 16 days ago - Pushed at: 16 days ago - Stars: 0 - Forks: 0

ArcInstitute/ScreenPro2

Flexible analysis of high-content CRISPR screening

Language: Python - Size: 3.53 MB - Last synced at: 5 days ago - Pushed at: 20 days ago - Stars: 29 - Forks: 6

YichaoOU/HemTools

HemTools: a collection of NGS pipelines and bioinformatic analyses

Language: Python - Size: 876 MB - Last synced at: 18 days ago - Pushed at: 18 days ago - Stars: 69 - Forks: 21

open2c/bioframe

Genomic interval operations on Pandas DataFrames

Language: Python - Size: 3.14 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 183 - Forks: 37

kkokay07/pq-genetics

Repository for population genetics and quantitative genetics metrics implementarion and visualization

Language: Jupyter Notebook - Size: 198 KB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 1 - Forks: 0

NBISweden/workshop-ngsintro

Workshop • Intro to Bioinformatics using NGS data • 5 days

Language: HTML - Size: 497 MB - Last synced at: 24 days ago - Pushed at: 24 days ago - Stars: 14 - Forks: 7

Alepidoptera7/mtReptile-

Files pertaining to the processing of NGS data in .fasta.gz format for the purposes of identifying the genomic sequences which belong to either of the tuataras dual mitochondrial genomes.

Language: Python - Size: 26.4 KB - Last synced at: 24 days ago - Pushed at: 25 days ago - Stars: 0 - Forks: 0

Alepidoptera7/MissingMotif

Determines the most probable sequences missing from a greater set of genomic reads.

Language: Python - Size: 7.81 KB - Last synced at: 24 days ago - Pushed at: 25 days ago - Stars: 0 - Forks: 0

RIVM-bioinformatics/ViroConstrictor

ViroConstrictor is a pipeline designed to process raw FastQ data from viral amplicon-based sequencing and generate biologically correct consensus sequences of the given viral genome

Language: Python - Size: 3.16 MB - Last synced at: 15 days ago - Pushed at: 18 days ago - Stars: 6 - Forks: 2

RIVM-bioinformatics/AmpliGone

A tool in order to accurately remove primer sequences from NGS reads in an amplicon experiment

Language: Python - Size: 2.71 MB - Last synced at: 14 days ago - Pushed at: 26 days ago - Stars: 16 - Forks: 0

RiyaDua/Oral_cancer_gene_identification

This project was my Master's (Biotechnology) Thesis project where we aimed to develop a machine learning model that identifies Oral cancer candidate genes.

Language: R - Size: 32.2 KB - Last synced at: 28 days ago - Pushed at: 28 days ago - Stars: 0 - Forks: 0

NagaComBio/TiNDA

Tumor in normal detection

Language: R - Size: 1.23 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 3 - Forks: 1

adrientaudiere/MiscMetabar

R package MiscMetabar: Miscellaneous functions for metabarcoding analysis

Language: R - Size: 334 MB - Last synced at: 5 days ago - Pushed at: 18 days ago - Stars: 17 - Forks: 0

mobidic/SEAL

SEAL db - Simple, Efficient And Lite database for NGS

Language: HTML - Size: 16.8 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 10 - Forks: 1

nali321/Sequence2Branches

Sequence2Branches: Creating a species-level phylogenetic tree from paired FASTQ reads

Language: Python - Size: 81.1 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 0

imjiaoyuan/papers-rep

Collection of bioinformatics analysis code and replication records for academic papers

Language: R - Size: 21.3 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 4 - Forks: 8

BU-ISCIII/iskylims

is an open-source LIMS (laboratory Information Management System) for Next Generation Sequencing sample management, statistics and reports, and bioinformatics analysis service management.

Language: Python - Size: 22.6 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 73 - Forks: 36

ishinder/EASTR

Emending Alignment of Spliced Transcript Reads

Language: Python - Size: 334 KB - Last synced at: 17 days ago - Pushed at: about 2 months ago - Stars: 11 - Forks: 1

czheluo/MBSA

Multple methods for BSA Pipeline

Language: R - Size: 2.41 MB - Last synced at: 25 days ago - Pushed at: over 5 years ago - Stars: 7 - Forks: 4

amarinderthind/RNA-seq-tutorial-for-gene-differential-expression-analysis

This RNAseq data analysis tutorial is created for educational purpose

Language: R - Size: 2.57 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 30 - Forks: 13

Genometric/MSPC

Using combined evidence from replicates to evaluate ChIP-seq peaks

Language: C# - Size: 21.9 MB - Last synced at: 14 days ago - Pushed at: 19 days ago - Stars: 20 - Forks: 10

BehRoooz/SRR14294834-scRNA-Seq-Data-Anaysis

Analysis of Single-Cell RNA data from SRR14294834 in peripheral blood mononuclear cells in severe asthma

Language: R - Size: 815 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

Geo-omics/scripts

Metagenomic pipeline and other general scripts used in the lab.

Language: Perl - Size: 11.1 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 35 - Forks: 22

dandyrilla/dandyrilla.github.io

Personal blog on computational biology and pathology

Language: SCSS - Size: 10.9 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

MiriamMarinS/ampAnalysis

Analysis of CRISPR-mediated edits in NGS amplicon sequences of multi-copy gene families.

Language: Python - Size: 804 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

iliapopov17/NGS-Handbook

🧐Handbook for NGS data analysis

Language: HTML - Size: 72.6 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

maxsonBraunLab/atac_seq

process and analyze paired-end ATAC-Seq data

Language: R - Size: 554 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 3 - Forks: 1

soedinglab/BaMMmotif2

Bayesian Markov Model motif discovery tool version 2 - An expectation maximization algorithm for the de novo discovery of enriched motifs as modelled by higher-order Markov models.

Language: C++ - Size: 9.23 MB - Last synced at: 22 days ago - Pushed at: about 4 years ago - Stars: 13 - Forks: 5

sib-swiss/NGS-variants-training

GitHub for the SIB courses NGS - Genome variant analysis

Language: Shell - Size: 69.4 MB - Last synced at: 13 days ago - Pushed at: 4 months ago - Stars: 25 - Forks: 9

pfcv99/metrics_app

Metrics App is a bioinformatics application developed in Python and Streamlit for calculate Depth of Coverage and Breadth of Coverage from BAM/CRAM files.

Language: Python - Size: 651 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

TomKellyGenetics/graphsim

R package: Simulate Expression data from igraph network using mvtnorm (CRAN; JOSS)

Language: R - Size: 35.8 MB - Last synced at: 5 days ago - Pushed at: over 2 years ago - Stars: 24 - Forks: 7

A reproducible RNA-Seq analysis pipeline for Staphylococcus aureus under antibiotic stress, utilizing Nextflow and Singularity. It involves genome mapping, read counting, and statistical analysis to identify differentially expressed genes (DEGs) and generates key visualizations.

Language: R - Size: 158 KB - Last synced at: about 1 month ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

pritampanda15/NGS-Workflows

Next-generation Sequencing workflows

Language: Jupyter Notebook - Size: 275 MB - Last synced at: 3 days ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

zhukovanadezhda/zhukovanadezhda

Size: 43 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

lucianhu/Masterarbeit

Leveraging WES short reads for PAN-EXOME creation and analysis.

Language: WDL - Size: 18.6 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

praneet1988/ELeFHAnt

Ensemble Learning for Harmonization and Annotation of Single Cells (ELeFHAnt) provides an easy to use R package for users to annotate clusters of single cells, harmonize labels across single cell datasets to generate a unified atlas and infer relationship among celltypes between two datasets. It uses an ensemble of three machine learning classifiers 1) RF 2) SVM and 3) LR

Language: R - Size: 61.2 MB - Last synced at: 5 months ago - Pushed at: almost 3 years ago - Stars: 20 - Forks: 6

IRI-UW-Bioinformatics/flu-ngs

NGS pipeline for influenza virus libraries

Language: Python - Size: 135 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 2 - Forks: 0

BU-ISCIII/bacterial_wgs_training

In this training course you will find theory and practice material for introducing yourself to wgs analysis for bacterial, including outbreak investigation.

Language: HTML - Size: 157 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 2 - Forks: 0

haseebmanzur/HackBio-Cancer-Internship

Here is my participation to the 2024 edition of the HackBio Internship (AMR in cancer track).

Language: R - Size: 1.07 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

DeplanckeLab/BeversLitovchenko2018

Source code to support the paper: "Extensive mitochondrial population structure and haplotype-specific variation in metabolic phenotypes in the Drosophila Genetic Reference Panel"

Language: R - Size: 122 KB - Last synced at: 5 months ago - Pushed at: over 2 years ago - Stars: 3 - Forks: 0

CEGRcode/scriptmanager

Language: Java - Size: 71.3 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 14 - Forks: 5

MitiushkinaNV/RACE_NGS

Python scripts for design of 5'/3' RACE-based NGS panels, and the following data analysis

Language: Python - Size: 67.4 KB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0

mskcc/facets2n

Algorithm to implement Fraction and Allelic Copy number Estimate from Tumor/normal Sequencing using unmatched normal sample(s) for log ratio calculations

Language: R - Size: 240 MB - Last synced at: 26 days ago - Pushed at: over 1 year ago - Stars: 11 - Forks: 0

CenterForMedicalGeneticsGhent/WisecondorX Fork of VUmcCGP/wisecondor

WisecondorX — An evolved WISECONDOR

Language: Python - Size: 35.8 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 94 - Forks: 41

sunyumail93/easyRNAseqDE

An R package for RNAseq differential expression analysis and visualization, in an easy and reproducible way.

Language: R - Size: 55.5 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 4 - Forks: 0

geniusphil/2024_digiplus_talent

2024 DIGI+ Talent跨域數位人才加速躍升計畫

Language: Shell - Size: 50 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 1 - Forks: 0

groverkaushal/Varying_kmer_effect_in_denovo_assembly

This project aims to observe the effect of selecting different kmer length parameter in 2 different de novo genome assembly tools - AbySS and Velvet.

Language: Python - Size: 1.45 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0

slowkow/saturation

:sponge: Estimate sequencing saturation for GEX, VDJ, and ADT data from the 10x Genomics platform.

Language: R - Size: 61.5 KB - Last synced at: 22 days ago - Pushed at: about 2 years ago - Stars: 5 - Forks: 1

hyunhwan-jeong/SalmonTE

SalmonTE is an ultra-Fast and Scalable Quantification Pipeline of Transpose Element (TE) Abundances

Language: Jupyter Notebook - Size: 258 MB - Last synced at: 6 months ago - Pushed at: over 2 years ago - Stars: 81 - Forks: 23

afrendeiro/toolkit

A toolkit for NGS analysis with Python

Language: Python - Size: 1.56 MB - Last synced at: 15 days ago - Pushed at: over 2 years ago - Stars: 14 - Forks: 4

DasProsad/codon_wise_ABE_editing

Script to quantify codon frequency after ABE-based editing

Language: Python - Size: 10.7 KB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 0

GeneMAP-Research/genemap-research.github.io

Genetic Medicine of African Populations

Size: 1.65 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 1 - Forks: 1

dohlee/hiv1-rloop

💻 Analysis codes and bioinformatic pipelines for paper "HIV-1-induced host genomic R-loops dictate HIV-1 integration site selection"

Language: Python - Size: 1.6 MB - Last synced at: about 2 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

LOVDnl/LOVDplus

LOVD+ -- LOVD for diagnostics: analysis of whole-exome data using LOVD.

Language: PHP - Size: 25.5 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 4 - Forks: 1

Abhishekapriya/ChIPSeqAnalysis

This repo contains the pipeline and methodology as well as results of the Chip-seq analysis project

Language: Shell - Size: 3.64 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

aobermayer4/ComputationalGenomics

Repository containing various RNA-seq, ChIP-seq, and 16S-seq analysis pipelines run through R

Language: R - Size: 3.01 MB - Last synced at: 11 months ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 0

aobermayer4/NGSDataParsing

Various scripts for working with NGS data in file formats such as VCF, BAM/SAM, and JSON

Language: Python - Size: 45.9 KB - Last synced at: 11 months ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 0

gitHBDX/TransfoRNA

TransfoRNA: Navigating the Uncertainties of Small RNA Annotation with an Adaptive Machine Learning Strategy

Language: Python - Size: 14.1 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 20 - Forks: 1

Crazzy-Rabbit/Script-in-Bio

生物信息学分析中用到的脚本

Language: Jupyter Notebook - Size: 9.86 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 8 - Forks: 5

lucianhu/Bash-script-DNA-Sequence

Linux command-line to analyse next-generation sequencing (NGS) data

Size: 103 KB - Last synced at: 12 months ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 0

uclahs-cds/package-OmicsQC

Aggregation of QC metrics and outlier nomination for multi-sample studies

Language: R - Size: 9.13 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 0 - Forks: 0

BiomedicalSciences/learning-git

Language: HTML - Size: 5.86 KB - Last synced at: 10 months ago - Pushed at: about 3 years ago - Stars: 2 - Forks: 0

esohkevin/esohkevin.github.io

esohinformatics

Size: 25.1 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

niekwit/cut_and_run

Snakemake workflow for Cut & Run

Language: Python - Size: 72.4 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

ShrutiBaikerikar/machine-learning-bioinformatics-paper-implementations

This repository covers research paper implementations in the field of Genomics, Next Generation Sequencing, Bioinformatics and Machine Learning.

Language: Python - Size: 4.2 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

RIVM-bioinformatics/SARS2seq

SARS2seq is a pipeline designed to process raw FastQ data from targeted SARS-CoV-2 sequencing and generate biologically correct consensus sequences of the SARS-CoV-2 genome.

Language: Python - Size: 1.41 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 6 - Forks: 0

florez-alberto/mock-fastq-generator

Generates randomly generated fastQ files from a template and upstream sequence.

Language: Python - Size: 139 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

srikanth-srinvas/MultiPolish-Dragonflye-Evaluation

A repository to automate genome assembly evaluation and benchmarking. Utilize scripts for Dragonflye with diverse polishing models on Illumina and Nanopore reads to fine-tune genome assemblies

Language: Python - Size: 67.4 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

harbourlab/SparK

Publication quality NGS track plotting

Language: Python - Size: 3.34 MB - Last synced at: 10 months ago - Pushed at: almost 3 years ago - Stars: 102 - Forks: 20

jalwillcox/Get-STR-Extensions

This script takes advantage of read pairing in bam/cram files to identify the presence of STR extensions.

Language: Shell - Size: 137 KB - Last synced at: about 1 year ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

LorenaDerezanin/pipeline_test

Variant calling pipeline (Snakemake workflow)

Language: Python - Size: 1.14 MB - Last synced at: about 1 year ago - Pushed at: about 3 years ago - Stars: 1 - Forks: 0

lvn3668/naivevariantcaller_ECGR_variantdetection

Python code to detect ECGR Mutations; Takes a reference genome and bunch of reads as input and finds mutations (1-3 bp length) where number of supporting reads greater than 5

Language: Python - Size: 2.39 MB - Last synced at: about 1 year ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0

lvn3668/fastqcparser

Python code to compute adatper content in reads, kmer content, per-base-GC content (at a specific position in a read alignment, against reference genome), per base NC content (at a specific position in a read alignment against the reference genome), per base seq quality (across aligned reads), per base sequence content, per base quality scores, per tile sequence quality

Language: Python - Size: 12.7 KB - Last synced at: about 1 year ago - Pushed at: over 3 years ago - Stars: 3 - Forks: 1

bioinfo-pf-curie/mpiMarkDup

Language: C - Size: 23.2 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 1

gozdekb/gozdekb

Basic packages for amplicon-based sequencing analysis.

Size: 8.79 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

ncbi/cwl-ngs-workflows-cbb

A set of CWL tools and workflows used by NCBI Computational Biology Branch for NGS data analysis

Language: Common Workflow Language - Size: 629 KB - Last synced at: about 1 year ago - Pushed at: almost 2 years ago - Stars: 24 - Forks: 10

niaid/Genetic-Linkage-Analysis

Materials for ACE course on Genetic Linkage Analysis.

Language: R - Size: 19.7 MB - Last synced at: about 1 year ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 2

anand-imcm/pb-variant-call

Variant Calling and Annotation using PacBio Hi-Fi Reads

Language: WDL - Size: 59.6 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

NCI-CGR/HPV_low_VAF_SNV_prediction

Predicting true low-VAF SNVs in HPV using triplicate NGS samples and machine learning

Language: Jupyter Notebook - Size: 17.3 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

JhuangLab/BioInstaller

A comprehensive R package to construct interactive and reproducible biological data analysis applications based on the R platform

Language: R - Size: 2.92 MB - Last synced at: 5 months ago - Pushed at: over 2 years ago - Stars: 56 - Forks: 13

rezabehboudi/RPTRF

RPTRF: A Rapid Perfect Tandem Repeat Finder Tool for DNA Sequences

Language: C++ - Size: 854 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 4 - Forks: 1

Aniket7651/BIOINFORMATICS

Bioinformatics is a field of information technology and biological science, which use to managing, storing and analyzing these biological data such as DNA, RNA and protein, In this repository I'm use python to create various types of program for analyzing biological data

Language: Python - Size: 1.92 MB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0