high-throughput-sequencing

There are 1 repository under high-throughput-sequencing topic.

brentp / hts-nim
nim wrapper for htslib for parsing genomics data files
bioinformatics genomics high-throughput-sequencing htslib nim nim-lang
Language:Nim 153
guma44 / GEOparse
Python library to access Gene Expression Omnibus Database (GEO)
geo-database high-throughput-sequencing htseq microarray bioinformatics rna-sequencing rna-seq
Language:Jupyter Notebook 130
bioinform / varsim
VarSim: A high-fidelity simulation validation framework for high-throughput genome sequencing with cancer applications
simulation validation high-throughput-sequencing genomics
Language:Java 78
BioJulia / BioAlignments.jl
Sequence alignment tools
bam-files sam-files sequence-alignment sequence-analysis dna-sequences biology bioinformatics smith-waterman-alignment high-throughput-sequencing biojulia
Language:Julia 58
smortezah / smashpp
Find and visualize rearrangements in DNA sequences
alignment-free data-visualization dna-sequences genome-compression genome-rearrangment high-throughput-sequencing
Language:C++ 56
nunofonseca / fastq_utils
Validation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification.
sequencing fastq validation ngs high-throughput-sequencing fastq-filterpair umi single-cell drop-seq 10x umi-count digital-gene-expression dge barcodes scrna-seq fastq-files fastq-validation
Language:C 34
USDA-VS / vSNP
vSNP -- validate SNPs
snp pipeline genomics tuberculosis brucella analysis-pipeline mycobacterium-tuberculosis-complex snps whole-genome-sequencing high high-throughput-sequencing bam-files vcf phylogenetics freebayes wgs
Language:Python 19
brentp / bigwig-nim
command-line querying+conversion of bigwigs and a nim wrapper for dpryan's libbigwig
bigwig nim nim-lang genomics bigbed high-throughput-sequencing
Language:Nim 16
brentp / genoiser
use the noise
genomics bioinformatics nim nim-lang high-throughput-sequencing
Language:Nim 15
PROBIC / mGEMS
mGEMS Genomic epidemiology with mixed samples
plate-sweep genomic-epidemiology metagenomics taxonomic-binning high-throughput-sequencing c-plus-plus
Language:C++ 14
weng-lab / umitools
A toolset for handling sequencing data with unique molecular identifiers (UMIs)
bioinformatics high-throughput-sequencing rna-seq small-rna unique-molecular-identifier umi
Language:Python 14
Biochemistry1-FFM / uORF-Tools
uORF-Tools are a workflow and a collection of tools for the analysis of 'Upstream Open Reading Frames' (short uORFs)
bioinformatics high-throughput-sequencing snakemake ribosome-profiling
Language:Python 13
edgardomortiz / Captus
Assembly of Phylogenomic Datasets from High-Throughput Sequencing data
ngs phylogenomics alignment genome-skimming high-throughput-sequencing hybridization-capture next-generation-sequencing phylogenetics rna-seq whole-genome-sequencing phylotranscriptomics orthologs paralogs target-capture busco-lineages busco-orthologs bioinformatics
Language:Python 13
PROBIC / mSWEEP
mSWEEP High-resolution sweep metagenomics using fast probabilistic inference
plate-sweep metagenomics taxonomic-profiling high-throughput-sequencing c-plus-plus
Language:C++ 13
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.
bayesian-inference bioinformatics-pipeline hidden-markov-model high-throughput-sequencing rna-structural-analysis
Language:HTML 10
pombo-lab / gamtools
Processing, quality control and analysis of GAM datsets
python python3 python2 molecular-biology high-throughput-sequencing chromatin
Language:Python 9
biomedicalinformaticsgroup / Sargasso
Sargasso disambiguates mixed-species high-throughput sequencing data.
bioinformatics high-throughput-sequencing rna-seq chip-seq atac-seq
Language:Python 8
zavolanlab / htsinfer
Infer metadata for your downstream analysis straight from your RNA-seq data
bioinformatics ngs high-throughput-sequencing inference hacktoberfest
Language:Python 8
3DGenomes / binless
Resolution-independent normalization of Hi-C data
hi-c normalization binless fused-lasso generalized-additive-models high-throughput-sequencing cpp11 rcpp r
Language:C++ 7
brentp / bpbio
basepair bio: a single binary with many useful genomics subtools.
genomics genomics-visualization cram bam structural-variation high-throughput-sequencing
Language:Nim 6
IgGeneUsage
snaketron / IgGeneUsage
Comparison of gene usage in immune repertoires under different biological conditions
immune-repertoires differential-gene-expression high-throughput-sequencing immunoinformatics immunological-bioinformatics vdj-recombination differential-analysis tcr-repertoire bcr-repertoire b-cell-receptor immunology immunoglobulin immunogenomics immune-repertoire immune-repertoire-analysis
Language:R 6
zhangchonglab / CRISPRi-functional-genomics-in-prokaryotes
python microbiology genomics high-throughput-sequencing
Language:Python 6
brentp / d4-nim
nim-lang wrapper for https://github.com/38/d4-format
bioinformatics genomics high-throughput-sequencing
Language:Nim 4
ExpoSeq
DigBioLab / ExpoSeq
ExpoSeq is a pipeline to process and analyze in various visualizations ngs data from phage display campaigns
ngs-pipeline phage-display clustering high-throughput-sequencing rnaseq antibody-sequencing
Language:HTML 3
gear-genomics / bgen
Barcode Generator
dna dna-barcode dna-sequences dna-sequencing gear-genomics genomics high-throughput-sequencing
Language:JavaScript 3
pmenzel / bam-to-clusters
high-throughput-sequencing cluster coverage
Language:C 2
USDA-VS / vSNP3
vSNP -- validate SNPs
bam-files snps analysis-pipeline brucella freebayes genomics high-throughput-sequencing influenza mycobacterium-tuberculosis-complex phylogenetics pipeline sars-cov-2 tuberculosis vcf-files wgs whole-genome-sequencing mycobacterium-bovis mycobacterium-bovis-af2122 bwa-mem
Language:Python 2
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.
2nd-3rd-4th-generation bioinformatics dna dna-rna-protein-modifications epigenome epitranscriptome high-throughput-sequencing perl-r-python-shell pipelines protein rna
Language:Perl 1
HMU-BioServer / ExMdb
All codes about ExMdb data processing
database exosomes high-throughput-sequencing scrna-seq
Language:R 1
kevin-fang / high-throughput-febio
Distributed iterative finite element analysis with high throughput computing
finite-element-analysis condor docker febio high-throughput-sequencing
Language:Python 1
mccahill / jupyter-HTS-2017
Jupyter server for Duke Biostatistics and Bioinformatics high-throughput sequencing and analysis workshop summer 2017
biostatistics bioinformatics high-throughput-sequencing jupyter
Language:Jupyter Notebook 1
tjh48 / segmentSeq
This package creates segmentation of the genome into regions of biological significance from high-throughput sequencing data.
bioconductor-package smallrna-seq methylation high-throughput-sequencing locus-map
Language:R 1
zavolanlab / multiqc-plugins
Custom plugins for the MultiQC tool.
bioinformatics bioinformatics-tool high-throughput-sequencing
Language:HTML 1
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.
bioinformatics high-throughput-sequencing quality-control rna-seq
Language:Python 1
gerverska / fun-gi
hamPCR + Douglas-fir + needle fungi
fungi metabarcoding plant-microbe-interactions amplicon-sequencing high-throughput-sequencing microbiome-analysis endophyte hampcr compositional-data-analysis microbiome mycobiome leaves
Language:HTML 0
Yudongfang-Qin / Peak-Caller-2022
Sequence peak caller
bio bioinformatics high-throughput-sequencing r macsii