brentp/hts-nim

nim wrapper for htslib for parsing genomics data files

Language: Nim - Size: 1.71 MB - Last synced at: about 1 month ago - Pushed at: 8 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: 8 days ago - Pushed at: 9 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: 8 days ago - Pushed at: 9 months ago - Stars: 62 - Forks: 24

smortezah/smashpp

Find and visualize rearrangements in DNA sequences

Language: C++ - Size: 760 MB - Last synced at: 10 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: 5 months ago - Pushed at: 9 months ago - Stars: 34 - Forks: 15

edgardomortiz/Captus

Assembly of Phylogenomic Datasets from High-Throughput Sequencing data

Language: Python - Size: 78.1 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 25 - Forks: 6

USDA-VS/vSNP

vSNP -- validate SNPs

Language: Python - Size: 68.5 MB - Last synced at: about 14 hours ago - Pushed at: 7 months ago - Stars: 20 - 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: 10 days ago - Pushed at: almost 5 years ago - Stars: 16 - Forks: 2

brentp/genoiser

use the noise

Language: Nim - Size: 1.94 MB - Last synced at: 10 days 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: 15 days ago - Pushed at: almost 7 years ago - Stars: 15 - Forks: 4

zavolanlab/htsinfer

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

Language: Python - Size: 8.32 MB - Last synced at: about 1 month ago - Pushed at: 5 months ago - Stars: 14 - Forks: 22

PROBIC/mGEMS

mGEMS Genomic epidemiology with mixed samples

Language: C++ - Size: 191 KB - Last synced at: 8 months ago - Pushed at: 8 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: 11 months ago - Pushed at: 11 months 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: over 5 years ago - Stars: 13 - Forks: 4

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: about 1 month 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: about 4 hours ago - Pushed at: almost 2 years ago - Stars: 9 - Forks: 14

USDA-VS/vSNP3

vSNP -- validate SNPs

Language: Python - Size: 5.82 MB - Last synced at: 23 days ago - Pushed at: 23 days ago - Stars: 8 - Forks: 2

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: over 5 years ago - Stars: 7 - Forks: 2

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: 8 days 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: about 1 month ago - Pushed at: almost 6 years ago - Stars: 6 - Forks: 2

nolan-h-hamilton/Consenrich

Genome-wide extraction of reproducible continuous signals hidden in noisy multisample functional genomics data

Language: Python - Size: 137 MB - Last synced at: 7 days ago - Pushed at: 8 days ago - Stars: 5 - Forks: 1

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: about 1 month ago - Pushed at: 5 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: 7 days ago - Pushed at: 9 months ago - Stars: 4 - Forks: 2

gear-genomics/bgen

Barcode Generator

Language: JavaScript - Size: 459 KB - Last synced at: about 1 year ago - Pushed at: over 1 year 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: over 1 year ago - Pushed at: over 1 year 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: 5 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: 12 days ago - Pushed at: over 3 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: about 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: over 7 years ago - Stars: 1 - 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: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

ndbrown6/innovation-lab

MSKCC CMO Innovation Lab

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

gerverska/fun-gi

hamPCR + Douglas-fir + needle fungi

Language: HTML - Size: 96.3 MB - Last synced at: 12 months ago - Pushed at: about 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: almost 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: about 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: about 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: about 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: about 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: about 2 years ago - Pushed at: about 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: 6 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: 2 months ago - Pushed at: about 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: over 1 year 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: over 1 year 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: about 2 years ago - Pushed at: almost 7 years ago - Stars: 0 - Forks: 0