This project contains all scripts and Java programs used for bioinformatics analyses in the publication: Seifert et al. (2018) Parental expression variation of small RNAs is negatively correlated with grain yield heterosis in a maize breeding population. Frontiers in Plant Science, doi: 10.3389/fpls.2018.00013
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Mirror script for Anaconda software repositories
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automated xtc to hdf5 conversion for lcls data. abstraction layer to separate out psana from science analysis
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snakemake pipeline for fastq to vcf
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A program that can extract the total forces and moments (for each load case) from the Freebody Loads .dat file generated by MSC. Patran
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Python code and source files used to identify and analyze PAM sequences for the complete NCBI spacerome
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Multiple Table Cell Selection
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Tool to identify unique primers for a given set of genomes
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The program compares two files at a time and does the following 1.Gathering metadata on the individual tables(column count,record count,list of columns with datatype etc) 2.Identifying matching columns between tables based on names as well as data. Using machine learning, we are handling syntactic as well as semantic variations of column names for accurate matching. 3. Finding duplicate columns in single table with the option to deduplicate if required 4. Finding columns with missing data/null values.
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G4Catchall is a python package designed to scan given DNA/RNA sequences for G-quadruplexes with or without atypical features
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Experimental metagenomic workflow
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Profiling Protein Structures from Protein Data Bank and integrate various resources.🏄♂️
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Break Rates Across the Genome - a phylogenomic tool for estimating the rearrangement rate across the genome.
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Gdal/OGR script for processing large amount of files
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Pipeline for ASE (allele specific expression) using competitive alignment to diploid genome
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Imports GPW (Warsaw Stock Exchange) rates from Bossa.pl metastock files
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AltamISA: a Python API for ISA-Tab files
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A Python notebook to create .loom files and extend them with other data e.g.: SCENIC regulons, Seurat clusters and markers, compatible with SCope
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Metagenomic Integron-associated Gene finder
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There are many ways to write a code for a particular task. This project starts with (may be updated) 28 ways to generate Fibonacci sequence in Python, includes using list, tuple, generator, etc. This is followed by another task, random sampling, (may also be updated) 20 ways to random sampling from a set of data.
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DEWE (Differential Expression Workflow Executor) is an open source application for easily executing Differential Expression analyses in RNA-Seq data.
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Structural variant analyzer for data visualization on VariantMap
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The repository for 'jipci', the Just Intonation Pansophical Conversion Instrument.
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Bioinformatics Programming Class
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Scripts to perform photometry and apply corrections
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Web application for gene curation.
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Python 3.6 library and command line tool for Cinema specifications A and D. http://cinemascience.org
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A filtering pipeline for producing a callset of somatic mutations.
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Scripts to do deeper analysis of 23 and me raw genome file.
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A tool for filtering variants from all2all comparison of multiple clones or single cells
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Integration of pathway-related information from MSigDB in BEL
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cell component for smartbox.io
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GWAS-admixed-population-simulatorby asmanouira
Python 
2 Version:Current
License: No License (No License)
License: No License (No License)Simulating GWAS data in PLINK format with GWAsimulator tool using Hapmap3 data
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Finding Hidden Messages in DNA (Bioinformatics I)
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Learning a genome-wide score of conservation at the functional genomics level between human and mouse
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A simple filter to annotate and filter somatic or germline variants based on their observed allele counts in ExAC
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Benchmarking ChIP-seq peak callers
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Amplicon sequencing workflow with snakemake and dada2
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Tools for enhancing efficiency of computational chemistry workflows.
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TIP_finder: Transposable element Insertion Polymorphism Finder for huge genomic datasets
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Command-line app retrieves genetic data from the 23andMe API and analyzes for Neanderthal variant matches.
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Multi-sample change detection in Hi-C patterns
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snp_extraction_from_alignmentsby tobiashofmann88
Python 2 Version:Current License: No License (No License)
License: No License (No License)This repository contains tools for the extraction of Single Nucleotide Polymorphisms (SNPs) from multiple sequence alignments.
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A repository for all WeiFund related data schemas
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An ILP algorithm for sorting cancer karyotypes. "Sorting cancer karyotypes using double-cut-and-joins, duplications and deletions", R. Zeira and R. Shamir, Bioinformatics, bty381, 2018. https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty381/4992148
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Normalize bedgraph files
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srna-heterosisby fseifert-uhh
This project contains all scripts and Java programs used for bioinformatics analyses in the publication: Seifert et al. (2018) Parental expression variation of small RNAs is negatively correlated with grain yield heterosis in a maize breeding population. Frontiers in Plant Science, doi: 10.3389/fpls.2018.00013
Java 2Updated: 3 y ago License: Strong Copyleft (GPL-3.0)
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conda-repoby gpcimino
Mirror script for Anaconda software repositories
Python 2Updated: 5 y ago License: Permissive (Apache-2.0)
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auto_xtc_hdf5_converterby sioan
automated xtc to hdf5 conversion for lcls data. abstraction layer to separate out psana from science analysis
Python 2Updated: 4 y ago License: No License (No License)
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potato-mappingby kramundson
snakemake pipeline for fastq to vcf
Python 2Updated: 4 y ago License: No License (No License)
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F
Freebody_Loads_Extractionby oncosmin
A program that can extract the total forces and moments (for each load case) from the Freebody Loads .dat file generated by MSC. Patran
Python 2Updated: 6 y ago License: Permissive (MIT)
2Updated: 6 y ago License: Permissive (MIT)Support
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C
CASPERpamby TrinhLab
Python code and source files used to identify and analyze PAM sequences for the complete NCBI spacerome
Python 2Updated: 4 y ago License: No License (No License)
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multi-cell-selectionby Zerocool27
Multiple Table Cell Selection
JavaScript 2Updated: 6 y ago License: No License (No License)
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PCR-PrimerFinderby annagaines
Tool to identify unique primers for a given set of genomes
Python 2Updated: 4 y ago License: No License (No License)
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Data-Profiling-Toolby rounayak
The program compares two files at a time and does the following 1.Gathering metadata on the individual tables(column count,record count,list of columns with datatype etc) 2.Identifying matching columns between tables based on names as well as data. Using machine learning, we are handling syntactic as well as semantic variations of column names for accurate matching. 3. Finding duplicate columns in single table with the option to deduplicate if required 4. Finding columns with missing data/null values.
Python 2Updated: 3 y ago License: No License (No License)
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G4Catchallby odoluca
G4Catchall is a python package designed to scan given DNA/RNA sequences for G-quadruplexes with or without atypical features
Python 2Updated: 3 y ago License: No License (No License)
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metagoby jordangumm
Experimental metagenomic workflow
Python 2Updated: 6 y ago License: No License (No License)
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COVID_pipeby mjsull
Python 2Updated: 3 y ago License: Strong Copyleft (GPL-3.0)
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pdb-profilingby NatureGeorge
Profiling Protein Structures from Protein Data Bank and integrate various resources.🏄♂️
Python 2Updated: 3 y ago License: Permissive (MIT)
2Updated: 3 y ago License: Permissive (MIT)Support
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ADACTby mujtahid-akon
PHP 2Updated: 4 y ago License: No License (No License)
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BRAGby channsoden
Break Rates Across the Genome - a phylogenomic tool for estimating the rearrangement rate across the genome.
Python 2Updated: 4 y ago License: Permissive (BSD-2-Clause)
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GeneticAncestryToolby npredey
Python 2Updated: 4 y ago License: No License (No License)
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mass_processingby BrunoCombal
Gdal/OGR script for processing large amount of files
Python 2Updated: 5 y ago License: Permissive (MIT)
2Updated: 5 y ago License: Permissive (MIT)Support
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ASE-CADGby everestial
Pipeline for ASE (allele specific expression) using competitive alignment to diploid genome
Python 2Updated: 2 y ago License: No License (No License)
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StockImporterby Lai90
Imports GPW (Warsaw Stock Exchange) rates from Bossa.pl metastock files
PHP 2Updated: 6 y ago License: No License (No License)
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altamisaby bihealth
AltamISA: a Python API for ISA-Tab files
Python 2Updated: 2 y ago License: Permissive (MIT)
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SCopeLoomPyby aertslab
A Python notebook to create .loom files and extend them with other data e.g.: SCENIC regulons, Seurat clusters and markers, compatible with SCope
Python 2Updated: 3 y ago License: Permissive (MIT)
2Updated: 3 y ago License: Permissive (MIT)Support
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migfinderby maribuon
Metagenomic Integron-associated Gene finder
Python 2Updated: 3 y ago License: Permissive (BSD-3-Clause)
2Updated: 3 y ago License: Permissive (BSD-3-Clause)Support
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nWaysby anbarief
There are many ways to write a code for a particular task. This project starts with (may be updated) 28 ways to generate Fibonacci sequence in Python, includes using list, tuple, generator, etc. This is followed by another task, random sampling, (may also be updated) 20 ways to random sampling from a set of data.
Python 2Updated: 5 y ago License: Permissive (MIT)
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deweby sing-group
DEWE (Differential Expression Workflow Executor) is an open source application for easily executing Differential Expression analyses in RNA-Seq data.
Java 2Updated: 5 y ago License: Strong Copyleft (GPL-3.0)
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variantbreakby cytham
Structural variant analyzer for data visualization on VariantMap
Python 2Updated: 3 y ago License: Strong Copyleft (GPL-3.0)
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jipciby misotanni
The repository for 'jipci', the Just Intonation Pansophical Conversion Instrument.
Python 2Updated: 3 y ago License: No License (No License)
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DAOPHOT-Scriptsby abichown
Scripts to perform photometry and apply corrections
Python 2Updated: 4 y ago License: No License (No License)
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gramene-curationby warelab
Web application for gene curation.
Python 2Updated: 4 y ago License: No License (No License)
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cinema_libby cinemascience
Python 3.6 library and command line tool for Cinema specifications A and D. http://cinemascience.org
Python 2Updated: 3 y ago License: Proprietary (Proprietary)
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SNVCurateby vymao
A filtering pipeline for producing a callset of somatic mutations.
Python 2Updated: 3 y ago License: No License (No License)
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genome-analysisby 0p1um
Scripts to do deeper analysis of 23 and me raw genome file.
Python 2Updated: 4 y ago License: No License (No License)
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All2by abyzovlab
A tool for filtering variants from all2all comparison of multiple clones or single cells
Python 2Updated: 3 y ago License: Permissive (MIT)
2Updated: 3 y ago License: Permissive (MIT)Support
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msigby bio2bel
Integration of pathway-related information from MSigDB in BEL
Python 2Updated: 3 y ago License: Permissive (MIT)
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cellby smartbox-io
cell component for smartbox.io
Ruby 2Updated: 6 y ago License: Permissive (Apache-2.0)
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GWAS-admixed-population-simulatorby asmanouira
Simulating GWAS data in PLINK format with GWAsimulator tool using Hapmap3 data
Python 2Updated: 4 y ago License: No License (No License)
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Bioinformatics-1by JoaoHenriqueOliveira
Finding Hidden Messages in DNA (Bioinformatics I)
Python 2Updated: 3 y ago License: No License (No License)
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LECIFby ernstlab
Learning a genome-wide score of conservation at the functional genomics level between human and mouse
Python 2Updated: 4 y ago License: Strong Copyleft (GPL-2.0)
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common_variant_filterby vanallenlab
A simple filter to annotate and filter somatic or germline variants based on their observed allele counts in ExAC
Python 2Updated: 3 y ago License: Strong Copyleft (GPL-2.0)
2Updated: 3 y ago License: Strong Copyleft (GPL-2.0)Support
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PeakCallingby skchronicles
Benchmarking ChIP-seq peak callers
Python 2Updated: 3 y ago License: Permissive (MIT)
2Updated: 3 y ago License: Permissive (MIT)Support
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dada2_snakemake_workflowby ramay
Amplicon sequencing workflow with snakemake and dada2
Python 2Updated: 3 y ago License: Permissive (MIT)
2Updated: 3 y ago License: Permissive (MIT)Support
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Eta_Scriptsby tjmustard
Tools for enhancing efficiency of computational chemistry workflows.
Python 2Updated: 4 y ago License: Proprietary (Proprietary)
2Updated: 4 y ago License: Proprietary (Proprietary)Support
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alphabetby Random-People
Python 2Updated: 4 y ago License: Permissive (WTFPL)
2Updated: 4 y ago License: Permissive (WTFPL)Support
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TIP_finderby simonorozcoarias
TIP_finder: Transposable element Insertion Polymorphism Finder for huge genomic datasets
Python 2Updated: 3 y ago License: No License (No License)
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23andMeNeanderthalby christineetaylor
Command-line app retrieves genetic data from the 23andMe API and analyzes for Neanderthal variant matches.
Python 2Updated: 5 y ago License: No License (No License)
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pareidoliaby koszullab
Multi-sample change detection in Hi-C patterns
Python 2Updated: 2 y ago License: Permissive (MIT)
2Updated: 2 y ago License: Permissive (MIT)Support
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snp_extraction_from_alignmentsby tobiashofmann88
This repository contains tools for the extraction of Single Nucleotide Polymorphisms (SNPs) from multiple sequence alignments.
Python 2Updated: 3 y ago License: No License (No License)
2Updated: 3 y ago License: No License (No License)Support
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weifund-schemaby weifund
A repository for all WeiFund related data schemas
JavaScript 2Updated: 7 y ago License: No License (No License)
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Sorting-Cancer-Karyotypesby Shamir-Lab
An ILP algorithm for sorting cancer karyotypes. "Sorting cancer karyotypes using double-cut-and-joins, duplications and deletions", R. Zeira and R. Shamir, Bioinformatics, bty381, 2018. https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty381/4992148
Python 2Updated: 4 y ago License: Permissive (BSD-3-Clause)
2Updated: 4 y ago License: Permissive (BSD-3-Clause)Support
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normalize_bedgraphby porchard
Normalize bedgraph files
Python 2Updated: 4 y ago License: No License (No License)
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