brentp/hts-nim

nim wrapper for htslib for parsing genomics data files

Language: Nim - Size: 1.71 MB - Last synced at: 3 months ago - Pushed at: 10 months ago - Stars: 155 - Forks: 27

guma44/GEOparse

Python library to access Gene Expression Omnibus Database (GEO)

Language: Jupyter Notebook - Size: 13.3 MB - Last synced at: 16 days ago - Pushed at: 11 months ago - Stars: 152 - Forks: 50

bioinform/varsim

VarSim: A high-fidelity simulation validation framework for high-throughput genome sequencing with cancer applications

Language: Java - Size: 45.6 MB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 79 - Forks: 30

BioJulia/BioAlignments.jl

Sequence alignment tools

Language: Julia - Size: 1.1 MB - Last synced at: 2 days ago - Pushed at: 10 months ago - Stars: 63 - Forks: 24

smortezah/smashpp

Find and visualize rearrangements in DNA sequences

Language: C++ - Size: 760 MB - Last synced at: 11 months ago - Pushed at: about 1 year ago - Stars: 56 - Forks: 12

nunofonseca/fastq_utils

Validation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification.

Language: C - Size: 82 MB - Last synced at: 6 months ago - Pushed at: 11 months ago - Stars: 34 - Forks: 15

edgardomortiz/Captus

Assembly of Phylogenomic Datasets from High-Throughput Sequencing data

Language: Python - Size: 78 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 26 - Forks: 6

USDA-VS/vSNP

vSNP -- validate SNPs

Language: Python - Size: 68.5 MB - Last synced at: 8 days ago - Pushed at: 9 months ago - Stars: 21 - Forks: 12

brentp/bigwig-nim

command-line querying+conversion of bigwigs and a nim wrapper for dpryan's libbigwig

Language: Nim - Size: 185 KB - Last synced at: about 2 months ago - Pushed at: about 5 years ago - Stars: 16 - Forks: 2

zavolanlab/htsinfer

Infer metadata for your downstream analysis straight from your RNA-Seq data

Language: Python - Size: 8.32 MB - Last synced at: 6 days ago - Pushed at: 7 months ago - Stars: 15 - Forks: 22

brentp/genoiser

use the noise

Language: Nim - Size: 1.94 MB - Last synced at: about 2 months ago - Pushed at: about 5 years ago - Stars: 15 - Forks: 0

weng-lab/umitools

A toolset for handling sequencing data with unique molecular identifiers (UMIs)

Language: Python - Size: 16.6 MB - Last synced at: 29 days ago - Pushed at: almost 7 years ago - Stars: 15 - Forks: 4

PROBIC/mGEMS

mGEMS Genomic epidemiology with mixed samples

Language: C++ - Size: 191 KB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 14 - Forks: 1

PROBIC/mSWEEP

mSWEEP High-resolution sweep metagenomics using fast probabilistic inference

Language: C++ - Size: 31.6 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 13 - Forks: 0

Biochemistry1-FFM/uORF-Tools

uORF-Tools are a workflow and a collection of tools for the analysis of 'Upstream Open Reading Frames' (short uORFs)

Language: Python - Size: 761 KB - Last synced at: over 1 year ago - Pushed at: almost 6 years ago - Stars: 13 - Forks: 4

USDA-VS/vSNP3

vSNP -- validate SNPs

Language: Python - Size: 5.85 MB - Last synced at: 22 days ago - Pushed at: 22 days ago - Stars: 11 - Forks: 2

marangiop/diff_BUM_HMM

Bayesian modelling approach for detecting RNA flexibility changes in high-throughput structure probing data under different conditions, based on an extension of the BUM-HMM method.

Language: HTML - Size: 101 MB - Last synced at: 3 months ago - Pushed at: over 2 years ago - Stars: 11 - Forks: 1

pombo-lab/gamtools

Processing, quality control and analysis of GAM datsets

Language: Python - Size: 840 KB - Last synced at: 16 days ago - Pushed at: almost 2 years ago - Stars: 9 - Forks: 14

biomedicalinformaticsgroup/Sargasso

Sargasso disambiguates mixed-species high-throughput sequencing data.

Language: Python - Size: 75.9 MB - Last synced at: over 1 year ago - Pushed at: about 3 years ago - Stars: 8 - Forks: 4

3DGenomes/binless

Resolution-independent normalization of Hi-C data

Language: C++ - Size: 558 MB - Last synced at: about 1 year ago - Pushed at: almost 6 years ago - Stars: 7 - Forks: 2

nolan-h-hamilton/Consenrich

Genome-wide extraction of real-valued signals hidden in noisy multisample HTS data

Language: Python - Size: 138 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 6 - Forks: 1

snaketron/IgGeneUsage

Comparison of gene usage in immune repertoires under different biological conditions

Language: R - Size: 281 MB - Last synced at: 8 days ago - Pushed at: about 2 months ago - Stars: 6 - Forks: 1

brentp/bpbio

basepair bio: a single binary with many useful genomics subtools.

Language: Nim - Size: 96.7 KB - Last synced at: 3 months ago - Pushed at: almost 6 years ago - Stars: 6 - Forks: 2

zhangchonglab/CRISPRi-functional-genomics-in-prokaryotes

Language: Python - Size: 104 MB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 5 - Forks: 3

brentp/d4-nim

nim-lang wrapper for https://github.com/38/d4-format

Language: Nim - Size: 26.4 KB - Last synced at: 3 months ago - Pushed at: 7 months ago - Stars: 4 - Forks: 1

DigBioLab/ExpoSeq

ExpoSeq is a pipeline to process and analyze in various visualizations ngs data from phage display campaigns

Language: HTML - Size: 221 MB - Last synced at: 22 days ago - Pushed at: 11 months ago - Stars: 4 - Forks: 2

gear-genomics/bgen

Barcode Generator

Language: JavaScript - Size: 567 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 3 - Forks: 2

ShangZhang/clipipe

CLIPipe(CLIP-seq Pipeline) is an integrated pipeline for analyzing CLIP sequencing data.

Language: HTML - Size: 246 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 2 - Forks: 3

HMU-BioServer/ExMdb

All codes about ExMdb data processing

Language: R - Size: 22.5 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

CTLife/Sequencing_DNA_RNA_Protein

Perl, R, Python, and Bash Shell source codes for high-throughput sequencing (the 2nd, 3rd, and 4th generation sequencing for DNA, RNA, and Protein) data analysis by integrating lots of open-source tools or softwares.

Language: Perl - Size: 355 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 0

zavolanlab/tin-score-calculation

Given a set of BAM files and a gene annotation BED file, calculates the Transcript Integrity Number (TIN) for each transcript.

Language: Python - Size: 2.14 MB - Last synced at: 6 months ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 1

zavolanlab/multiqc-plugins

Custom plugins for the MultiQC tool.

Language: HTML - Size: 1.56 MB - Last synced at: 27 days ago - Pushed at: almost 4 years ago - Stars: 1 - Forks: 0

tjh48/segmentSeq

This package creates segmentation of the genome into regions of biological significance from high-throughput sequencing data.

Language: R - Size: 4.35 MB - Last synced at: over 1 year ago - Pushed at: almost 7 years ago - Stars: 1 - Forks: 0

kevin-fang/high-throughput-febio

Distributed iterative finite element analysis with high throughput computing

Language: Python - Size: 90.8 KB - Last synced at: over 2 years ago - Pushed at: about 7 years ago - Stars: 1 - Forks: 1

pmenzel/bam-to-clusters

Language: C - Size: 7.81 KB - Last synced at: about 2 years ago - Pushed at: over 7 years ago - Stars: 1 - Forks: 0

mccahill/jupyter-HTS-2017

Jupyter server for Duke Biostatistics and Bioinformatics high-throughput sequencing and analysis workshop summer 2017

Language: Jupyter Notebook - Size: 377 KB - Last synced at: about 2 years ago - Pushed at: almost 8 years ago - Stars: 1 - Forks: 0

NIGMS/RNA-Methylation-with-MeRIP-seq

The MeRIP-seq data analysis tutorial is structured into four submodules, designed to comprehensively guide users through the complete workflow for RNA methylation analysis

Language: HTML - Size: 14 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 0 - Forks: 0

NIGMS/Transcriptome-Assembly-Refinement-and-Applications

In this module, you will learn how to use a Nextflow pipeline to assemble and annotate a novel transcriptome using RNA-seq data

Language: Jupyter Notebook - Size: 6.16 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 0 - Forks: 4

NIGMS/Population-Genomics-and-Phylogenetics-with-RADseq

This repository provides a comprehensive tutorial for phylogenetic analysis, covering data collection, sequence alignment, tree construction, and interpretation. It runs on AWS SageMaker using Jupyter notebooks and includes tools like MAFFT, Nextclade, and IQ-TREE.

Language: Jupyter Notebook - Size: 10.6 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 0 - Forks: 0

NIGMS/Bulk-and-Single-Cell-RNAseq

In this module, you will take a deeper look at RNA-sequencing using single-cell approaches and miRNA sequencing, and investigate their impacts on gene regulation

Language: Jupyter Notebook - Size: 6.34 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 0 - Forks: 0

NIGMS/Intro-to-Pangenomics

This repository provides a comprehensive module on graphical pangenomics, guiding users through building, indexing, mapping, and visualizing pangenome graphs. The module runs on Google Cloud Platform using Jupyter notebooks and includes tools like PGGB, vg, BLAST, and Bandage.

Language: HTML - Size: 22.4 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 0 - Forks: 0

NIGMS/16SrRNA-Microbial-Analysis

This repository provides a cloud-based learning module for microbial analysis of 16S rRNA sequencing data. It covers principles, data preprocessing, taxonomic classification, and diversity analysis using R and AWS SageMaker.

Language: HTML - Size: 31.5 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 0 - Forks: 0

SimonHegele/Bioinformatics-Lecture-Notebooks

A collection of jupyter notbooks containing summaries and implementations of mathematical concepts and algorithms presented in various lectures on bioinformatics and related subjects

Language: Jupyter Notebook - Size: 5.22 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

ndbrown6/innovation-lab

MSKCC CMO Innovation Lab

Language: Makefile - Size: 73.8 MB - Last synced at: almost 2 years ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 1

gerverska/fun-gi

hamPCR + Douglas-fir + needle fungi

Language: HTML - Size: 96.3 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

ZooPhy/radx

RADx-rad pipeline for metagenomic data and analysis of SARS-CoV-2 from wastewater

Language: Python - Size: 1.47 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

Yudongfang-Qin/Peak-Caller-2022

Sequence peak caller

Size: 2.07 MB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0

rancilhac/Museoscript

Script to process illumina reads from museum specimens

Language: Shell - Size: 224 KB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

jungsoh/high-throughput-sequence-data-handling-course

Material used for a course on handling high-throughput genomic data handling, covering DNA sequence assembly, RNA-seq data analysis, metagenomics, and read alignment

Language: HTML - Size: 28.3 MB - Last synced at: over 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

tare/raesymatto

Raesymatto: visualize genomic data

Language: Jupyter Notebook - Size: 85 KB - Last synced at: over 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

ElsevierSoftwareX/SOFTX_2020_130 Fork of refresh-bio/Whisper

Whisper 2: indel-sensitive short read mapping. To cite this software publication: https://www.sciencedirect.com/science/article/pii/S2352711021000376

Language: C++ - Size: 2.09 MB - Last synced at: over 2 years ago - Pushed at: about 4 years ago - Stars: 0 - Forks: 0

wanglab-upenn/HiPR

HiPR: High-throughput Probabilistic inference of RNA structure

Language: C++ - Size: 1.43 MB - Last synced at: over 2 years ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0

tjbencomo/ngs-pipeline-retired

NGS Processing Pipelines for WGS and WES data

Language: Python - Size: 91.8 KB - Last synced at: 7 months ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0

bmazoure/AssayCorrector

The AssayCorrector eliminates spatial bias in HTS assays using PMP methods.

Language: R - Size: 290 KB - Last synced at: about 1 year ago - Pushed at: almost 6 years ago - Stars: 0 - Forks: 0

pblischak/fluidigm2purc

Automated processing and haplotype inference for double-barcoded PCR amplicons

Language: Python - Size: 474 KB - Last synced at: 26 days ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0

tjh48/clusterSeq

Identification of clusters of co-expressed genes based on their expression across multiple (replicated) biological samples.

Language: R - Size: 837 KB - Last synced at: almost 2 years ago - Pushed at: almost 7 years ago - Stars: 0 - Forks: 0

tjh48/baySeq

This package identifies differential expression in high-throughput 'count' data, such as that derived from next-generation sequencing machines, calculating estimated posterior likelihoods of differential expression (or more complex hypotheses) via empirical Bayesian methods.

Language: R - Size: 1.07 MB - Last synced at: almost 2 years ago - Pushed at: almost 7 years ago - Stars: 0 - Forks: 2

MatthewWolff/CHTC

A series of scripts used for transferring and validating files with gluster, and for submitting condor jobs

Language: Shell - Size: 27.2 MB - Last synced at: over 2 years ago - Pushed at: about 7 years ago - Stars: 0 - Forks: 0