|
dimspy
|
public |
Python package for data processing of direct-infusion mass spectrometry-based metabolomics and lipidomics data
|
2023-06-16 |
|
r-phylobase
|
public |
Provides a base S4 class for comparative methods, incorporating one or more trees and trait data.
|
2023-06-16 |
|
r-oai
|
public |
A general purpose client to work with any 'OAI-PMH' (Open Archives Initiative Protocol for 'Metadata' Harvesting) service. The 'OAI-PMH' protocol is described at <http://www.openarchives.org/OAI/openarchivesprotocol.html>. Functions are provided to work with the 'OAI-PMH' verbs: 'GetRecord', 'Identify', 'ListIdentifiers', 'ListMetadataFormats', 'ListRecords', and 'ListSets'.
|
2023-06-16 |
|
r-rbison
|
public |
Interface to the 'USGS' 'BISON' (<https://bison.usgs.gov/>) 'API', a 'database' for species occurrence data. Data comes from species in the United States from participating data providers. You can get data via 'taxonomic' and location based queries. A simple function is provided to help visualize data.
|
2023-06-16 |
|
r-ecodist
|
public |
Dissimilarity-based analysis functions including ordination and Mantel test functions, intended for use with spatial and community data.
|
2023-06-16 |
|
r-rvertnet
|
public |
Retrieve, map and summarize data from the 'VertNet.org' archives (<http://vertnet.org/>). Functions allow searching by many parameters, including 'taxonomic' names, places, and dates. In addition, there is an interface for conducting spatially delimited searches, and another for requesting large 'datasets' via email.
|
2023-06-16 |
|
r-ridigbio
|
public |
An interface to iDigBio's search API that allows downloading specimen records. Searches are returned as a data.frame. Other functions such as the metadata end points return lists of information. iDigBio is a US project focused on digitizing and serving museum specimen collections on the web. See <https://www.idigbio.org> for information on iDigBio.
|
2023-06-16 |
|
r-geoaxe
|
public |
Split 'geospatial' objects into pieces. Includes support for some spatial object inputs, 'Well-Known Text', and 'GeoJSON'.
|
2023-06-16 |
|
illumiprocessor
|
public |
illumiprocessor is a tool to batch process illumina sequencing reads using the excellent trimmomatic package.
|
2023-06-16 |
|
r-wicket
|
public |
Utilities to generate bounding boxes from 'WKT' (Well-Known Text) objects and R data types, validate 'WKT' objects and convert object types from the 'sp' package into 'WKT' representations.
|
2023-06-16 |
|
r-adephylo
|
public |
Multivariate tools to analyze comparative data, i.e. a phylogeny and some traits measured for each taxa.
|
2023-06-16 |
|
snpsplit
|
public |
SNPsplit is an allele-specific alignment sorter which is designed to read in alignment files in SAM/BAM format and determine the allelic origin of reads that cover known SNP positions.
|
2023-06-16 |
|
womtool
|
public |
Command line utilities for interacting with WDL
|
2023-06-16 |
|
real
|
public |
REad ALigner for Next-Generation sequencing reads.
|
2023-06-16 |
|
r-propcis
|
public |
Computes two-sample confidence intervals for single, paired and independent proportions.
|
2023-06-16 |
|
bsmap
|
public |
BSMAP is a short reads mapping software for bisulfite sequencing reads.
|
2023-06-16 |
|
ngmerge
|
public |
Merging paired-end reads and removing sequencing adapters.
|
2023-06-16 |
|
cortex_con
|
public |
cortex_con (primary contact Mario Caccamo) is for consensus genome assembly
|
2023-06-16 |
|
esimsa
|
public |
Simple deconvolution of electrospray ionization peak lists
|
2023-06-16 |
|
idr-py
|
public |
Helper methods for accessing the Image Data Resource (IDR)
|
2023-06-16 |
|
spotyping
|
public |
SpoTyping: fast and accurate in silico Mycobacterium spoligotyping from sequence reads
|
2023-06-16 |
|
blobtools
|
public |
Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets
|
2023-06-16 |
|
cdna_cupcake
|
public |
cDNA_Cupcake is a miscellaneous collection of Python and R scripts used for analyzing sequencing data.
|
2023-06-16 |
|
riboraptor
|
public |
Python package to analyse ribosome profiling data
|
2023-06-16 |
|
erds
|
public |
Inferring copy number variants in high-coverage human genomes with next-generation sequencing data.
|
2023-06-16 |
|
r-genometricorr
|
public |
Genometric Correlation (GenometriCorr) is an R package for spatial correlation of genome-wide interval datasets.
|
2023-06-16 |
|
ctat-lncrna
|
public |
ctat-lncrna uses slncky
|
2023-06-16 |
|
realphy
|
public |
The Reference sequence Alignment based Phylogeny
|
2023-06-16 |
|
r-fmsb
|
public |
Several utility functions for the book entitled "Practices of Medical and Health Data Analysis using R" (Pearson Education Japan, 2007) with Japanese demographic data and some demographic analysis related functions.
|
2023-06-16 |
|
jali
|
public |
Alignment method for comparing a protein sequence to a protein family, represented by a multiple alignment. It can also be used for sensitive protein database searches. The algorithm is a generalization of the Smith-Waterman algorithm.
|
2023-06-16 |
|
biopet-vcfstats
|
public |
Vcfstats is a tool that can generate metrics from a vcf file.
|
2023-06-16 |
|
bibliospec
|
public |
The BiblioSpec Spetral Library tool suite
|
2023-06-16 |
|
perl-extutils-cbuilder
|
public |
Compile and link C code for Perl modules
|
2023-06-16 |
|
mmvc
|
public |
Call variants based on a Bayesian multinomial mixture model.
|
2023-06-16 |
|
ruby-dna-tools
|
public |
Various libraries containing useful functions for working with DNA sequences, written in ruby. Some tools are not specific to DNA.
|
2023-06-16 |
|
pbhoover
|
public |
Variant caller for legacy and low coverage Pacific Biosciences' long-read sequencing data
|
2023-06-16 |
|
perl-extutils-constant
|
public |
generate XS code to import C header constants
|
2023-06-16 |
|
perl-perl4-corelibs
|
public |
libraries historically supplied with Perl 4
|
2023-06-16 |
|
ac-diamond
|
public |
AC-DIAMOND is a DNA-protein alignment tool
|
2023-06-16 |
|
r-stampp
|
public |
Allows users to calculate pairwise Nei's Genetic Distances (Nei 1972), pairwise Fixation Indexes (Fst) (Weir & Cockerham 1984) and also Genomic Relationship matrixes following Yang et al. (2010) in mixed and single ploidy populations. Bootstrapping across loci is implemented during Fst calculation to generate confidence intervals and p-values around pairwise Fst values. StAMPP utilises SNP genotype data of any ploidy level (with the ability to handle missing data) and is coded to utilise multithreading where available to allow efficient analysis of large datasets. StAMPP is able to handle genotype data from genlight objects allowing integration with other packages such adegenet. Please refer to LW Pembleton, NOI Cogan & JW Forster, 2013, Molecular Ecology Resources, 13(5), 946-952. <doi
|
2023-06-16 |
|
rnaclust
|
public |
A tool for clustering of RNAs based on their secondary structures using LocARNA
|
2023-06-16 |
|
vqsr_cnn
|
public |
Variant quality score recalibration with Convolutional Neural Networks
|
2023-06-16 |
|
hanselx
|
public |
A graph-inspired data structure for determining likely chains of sequences from breadcrumbs of evidence
|
2023-06-16 |
|
brockman-pipeline
|
public |
Brockman Representation Of Chromatin by K-mers in Mark-Associated Nucleotides
|
2023-06-16 |
|
amused
|
public |
Auditing Motifs Using Statistical Enrichment & Depletion
|
2023-06-16 |
|
gretel
|
public |
An algorithm for recovering haplotypes from metagenomes
|
2023-06-16 |
|
comparative-annotation-toolkit
|
public |
A straightforward end-to-end pipeline that takes as input a HAL-format multiple whole genome alignment as well as a GFF3 file representing annotations on one high quality assembly in the HAL alignment, and produces a output GFF3 annotation on all target genomes chosen
|
2023-06-16 |
|
segtools
|
public |
a python package for analyzing genomic segmentations
|
2023-06-16 |
|
assemblerflow
|
public |
A Nextflow pipeline assembler for genomics. Pick your modules. Assemble them. Run the pipeline.
|
2023-06-16 |
|
satsuma2
|
public |
FFT cross-correlation based synteny aligner, (re)designed to make full use of parallel computing
|
2023-06-16 |
