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pyimagingmspec
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public |
Python library for processing imaging mass spectrometry data
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2023-06-16 |
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afplot
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public |
Plot allele frequencies in VCF files
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2023-06-16 |
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cgview
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public |
CGView is a Java package for generating high quality, zoomable maps of circular genomes.
Its primary purpose is to serve as a component of sequence annotation pipelines, as a
means of generating visual output suitable for the web.
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2023-06-16 |
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r-qtl
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public |
Analysis of experimental crosses to identify genes (called quantitative trait loci, QTLs) contributing to variation in quantitative traits.
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2023-06-16 |
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xunit-wrapper
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public |
Wrap python functions with a decorator to handle building XUnit reports
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2023-06-16 |
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aenum
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public |
Advanced Enumerations (compatible with Python's stdlib Enum), NamedTuples, and NamedConstants
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2023-06-16 |
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swiftlink
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public |
A multipoint parametric linkage analysis tool for large consanguineous pedigrees and is primarily targeted at pedigrees that cannot be analysed by a Lander-Green algorithm based program, i.e. many markers, but larger pedigrees.
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2023-06-16 |
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gfapy
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public |
Library for handling data in the GFA1 and GFA2 formats
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2023-06-16 |
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wheezy.template
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public |
A lightweight template library
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2023-06-16 |
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cyvcf
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public |
A cython wrapper around htslib built for fast parsing of Variant Call Format (VCF) files
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2023-06-16 |
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backports.unittest_mock
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public |
backports.unittest_mock
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2023-06-16 |
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sprai
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public |
Sprai (single-pass read accuracy improver) is a tool to correct sequencing errors in single-pass reads for de novo assembly. It is originally designed for correcting sequencing errors in single-molecule DNA sequencing reads, especially in Continuous Long Reads (CLRs) generated by PacBio RS sequencers. The goal of Sprai is not maximizing the accuracy of error-corrected reads; instead, Sprai aims at maximizing the continuity (i.e., N50 contig length) of assembled contigs after error correction.
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2023-06-16 |
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edd
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public |
Enriched domain detector for ChIP-seq data
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2023-06-16 |
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funcannot
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public |
Annotates cDNA, protein, mutation type, and other funcational changes to variants in a VCF file with pre-existing gene annotations (see:genepender).
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2023-06-16 |
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genepender
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public |
Annotates overlapping BED-defined regions to variants in a VCF file. Used primarily for providing a gene/exon context to variants (see:bedtarget).
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2023-06-16 |
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r-mqtl
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public |
mQTL provides a complete QTL analysis pipeline for metabolomic data. Distinctive features include normalisation using PQN approach, peak alignment using RSPA approach, dimensionality reduction using SRV approach and finally QTL mapping using R/qtl package.
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2023-06-16 |
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dupre
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public |
Duplicate rate estimation using linear programming and the hypergeometric distribution
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2023-06-16 |
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galaxy-ie-helpers
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public |
Helper scripts to work with Galaxy's Interactive Environments
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2023-06-16 |
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bioconductor-motifrg
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public |
A package for discriminative motif discovery, designed for high throughput sequencing dataset
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2023-06-16 |
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menetools
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public |
Python 3 Metabolic Network Topology Tools
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2023-06-16 |
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tablet
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public |
Tablet is a lightweight, high-performance graphical viewer for next generation sequence assemblies and alignments.
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2023-06-16 |
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tadtool
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public |
TADtool is an interactive tool for the identification of meaningful parameters in TAD-calling algorithms for Hi-C data
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2023-06-16 |
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barrnap-python
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public |
python package for Torsten Seemann's barrnap package for annotating rRNAs
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2023-06-16 |
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bioconductor-deseq
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public |
Differential gene expression analysis based on the negative binomial distribution
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2023-06-16 |
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r-argumentcheck
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public |
The typical process of checking arguments in functions is iterative. In this process, an error may be returned and the user may fix it only to receive another error on a different argument. 'ArgumentCheck' facilitates a more helpful way to perform argument checks allowing the programmer to run all of the checks and then return all of the errors and warnings in a single message.
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2023-06-16 |
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rabix-bunny
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public |
Open-source development kit for the Common Workflow Language from Seven Bridges. The Rabix executor Bunny, which can be used to execute apps locally from the command line.
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2023-06-16 |
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eagle
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public |
Eagle is a webtool for genome variants and snp analysis
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2023-06-16 |
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cosi2
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public |
cosi2 is an efficient coalescent simulator with support for selection, population structure, variable recombination rates, and gene conversion. It supports exact and approximate simulation modes.
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2023-06-16 |
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r-maldiquantforeign
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public |
Functions for reading (tab, csv, Bruker fid, Ciphergen XML, mzXML, mzML, imzML, Analyze 7.5, CDF, mMass MSD) and writing (tab, csv, mMass MSD, mzML, imzML) different file formats of mass spectrometry data into/from 'MALDIquant' objects.
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2023-06-16 |
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r-psych
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public |
A general purpose toolbox for personality, psychometric theory and experimental psychology. Functions are primarily for multivariate analysis and scale construction using factor analysis, principal component analysis, cluster analysis and reliability analysis, although others provide basic descriptive statistics. Item Response Theory is done using factor analysis of tetrachoric and polychoric correlations. Functions for analyzing data at multiple levels include within and between group statistics, including correlations and factor analysis. Functions for simulating and testing particular item and test structures are included. Several functions serve as a useful front end for structural equation modeling. Graphical displays of path diagrams, factor analysis and structural equation models are created using basic graphics. Some of the functions are written to support a book on psychometric theory as well as publications in personality research. For more information, see the <http://personality-project.org/r> web page.
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2023-06-16 |
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pyasp
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public |
A convenience wrapper for the ASP tools gringo, gringo4 and clasp.
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2023-06-16 |
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r-gam
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public |
No Summary
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2023-06-16 |
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r-gbm
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public |
An implementation of extensions to Freund and Schapire's AdaBoost algorithm and Friedman's gradient boosting machine. Includes regression methods for least squares, absolute loss, t-distribution loss, quantile regression, logistic, multinomial logistic, Poisson, Cox proportional hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss, and Learning to Rank measures (LambdaMart).
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2023-06-16 |
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r-qqman
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public |
Create Q-Q and manhattan plots for GWAS data from PLINK results.
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2023-06-16 |
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feht
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public |
A commandline program to automatically identify markers predictive of groups. Can be used with binary data, genomic (single nucleotide variant) data, or arbitrary character data.
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2023-06-16 |
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r-factominer
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public |
Exploratory data analysis methods to summarize, visualize and describe datasets. The main principal component methods are available, those with the largest potential in terms of applications: principal component analysis (PCA) when variables are quantitative, correspondence analysis (CA) and multiple correspondence analysis (MCA) when variables are categorical, Multiple Factor Analysis when variables are structured in groups, etc. and hierarchical cluster analysis.
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2023-06-16 |
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tqdist
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public |
computes the triplet distance between rooted trees in O(n log n) time and the quartet distance between unrooted trees in O(dn log n) time, where d degree of the tree with the smallest degree.
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2023-06-16 |
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yanagiba
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public |
Filter short or low quality Oxford Nanopore reads which have been basecalled with Albacore.
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2023-06-16 |
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graphprot
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public |
GraphProt is a tool for modelling binding preferences of RNA-binding proteins from high-throughput experiments such as CLIP-seq and RNAcompete.
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2023-06-16 |
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pyquant-ms
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public |
A framework for the analysis of quantitative mass spectrometry data
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2023-06-16 |
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ghm
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public |
A MOD-score analysis in which parametric LOD scores are maximized over the parameters of the trait model
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2023-06-16 |
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prestor
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public |
A prototype package for generating quality control plots from pRESTO output.
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2023-06-16 |
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lordec
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public |
A hybrid error correction program for long, PacBio reads
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2023-06-16 |
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bcftools-snvphyl-plugin
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public |
The SNVPhyl (Single Nucleotide Variant PHYLogenomics) pipeline is a pipeline for identifying Single Nucleotide Variants (SNV) within a collection\ of microbial genomes and constructing a phylogenetic tree. This package is the bcftools C plugin
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2023-06-16 |
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nucleoatac
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public |
Python package for calling nucleosomes using ATAC-Seq data. Also includes general scripts for working with paired-end ATAC-Seq data (or potentially other paired-end data).
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2023-06-16 |
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sift4g
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public |
SIFT 4G is a faster version of SIFT that enables us to scale up and provide SIFT predictions for more organisms.
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2023-06-16 |
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perl-io-gzip
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public |
Perl extension to provide a PerlIO layer to gzip/gunzip
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2023-06-16 |
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mapsembler2
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public |
Targeted assembly software
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2023-06-16 |
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graphicsmagick
|
public |
GraphicsMagick is the swiss army knife of image processing
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2023-06-16 |
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fwdpp
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public |
A C++ template library for forward-time population genetic simulation.
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2023-06-16 |
