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spine
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public |
Identification of conserved nucleotide core genome of bacteria and other small genome organisms
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2023-06-16 |
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r-kmsurv
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public |
Data sets and functions for Klein and Moeschberger (1997), "Survival Analysis, Techniques for Censored and Truncated Data", Springer.
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2023-06-16 |
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libmuscle
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public |
libMuscle header files.
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2023-06-16 |
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r-exactranktests
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public |
Computes exact conditional p-values and quantiles using an implementation of the Shift-Algorithm by Streitberg & Roehmel.
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2023-06-16 |
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r-km.ci
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public |
Computes various confidence intervals for the Kaplan-Meier estimator, namely Petos CI, Rothman CI, CI's based on Greenwoods variance, Thomas and Grunkemeier CI and the simultaneous confidence bands by Nair and Hall and Wellner.
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2023-06-16 |
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helperlibs
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public |
A collection of bioinformatics-related helper functions
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2023-06-16 |
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crispresso
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public |
A software pipeline for the analysis of targeted CRISPR-Cas9 sequencing data
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2023-06-16 |
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r-e1071
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public |
Functions for latent class analysis, short time Fourier transform, fuzzy clustering, support vector machines, shortest path computation, bagged clustering, naive Bayes classifier, ...
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2023-06-16 |
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r-fpc
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public |
Various methods for clustering and cluster validation. Fixed point clustering. Linear regression clustering. Clustering by merging Gaussian mixture components. Symmetric and asymmetric discriminant projections for visualisation of the separation of groupings. Cluster validation statistics for distance based clustering including corrected Rand index. Cluster-wise cluster stability assessment. Methods for estimation of the number of clusters: Calinski-Harabasz, Tibshirani and Walther's prediction strength, Fang and Wang's bootstrap stability. Gaussian/multinomial mixture fitting for mixed continuous/categorical variables. Variable-wise statistics for cluster interpretation. DBSCAN clustering. Interface functions for many clustering methods implemented in R, including estimating the number of clusters with kmeans, pam and clara. Modality diagnosis for Gaussian mixtures.
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2023-06-16 |
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r-rttf2pt1
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public |
Contains the program 'ttf2pt1', for use with the 'extrafont' package. This product includes software developed by the 'TTF2PT1' Project and its contributors.
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2023-06-16 |
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r-diptest
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public |
Compute Hartigan's dip test statistic for unimodality / multimodality and provide a test with simulation based p-values, where the original public code has been corrected.
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2023-06-16 |
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embl-api-validator
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public |
ENA flat file validator for submission
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2023-06-16 |
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r-trimcluster
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public |
Trimmed k-means clustering.
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2023-06-16 |
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r-micropan
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public |
A collection of functions for computations and visualizations of microbial pan-genomes.
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2023-06-16 |
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genonets
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public |
Framework for creating and analyzing genotype networks from data.
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2023-06-16 |
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embassy-phylip
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public |
embassy/emboss wrappers for phylip functions
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2023-06-16 |
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r-extrafontdb
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public |
Package for holding the database for the extrafont package
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2023-06-16 |
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pyquery
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public |
A jquery-like library for python
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2023-06-16 |
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maxentpy
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public |
maxentpy is a python wrapper for MaxEntScan to calculate splice site strength.
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2023-06-16 |
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r-flexclust
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public |
The main function kcca implements a general framework for k-centroids cluster analysis supporting arbitrary distance measures and centroid computation. Further cluster methods include hard competitive learning, neural gas, and QT clustering. There are numerous visualization methods for cluster results (neighborhood graphs, convex cluster hulls, barcharts of centroids, ...), and bootstrap methods for the analysis of cluster stability.
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2023-06-16 |
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tabix
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public |
C library and command line tools for high-throughput sequencing data formats.
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2023-06-16 |
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xcftools
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public |
Provides xcf2pnm, xcf2png, and xcfinfo binaries
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2023-06-16 |
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r-extrafont
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public |
Tools to using fonts other than the standard PostScript fonts. This package makes it easy to use system TrueType fonts and with PDF or PostScript output files, and with bitmap output files in Windows. extrafont can also be used with fonts packaged specifically to be used with, such as the fontcm package, which has Computer Modern PostScript fonts with math symbols. See https://github.com/wch/extrafont for instructions and examples.
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2023-06-16 |
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avro-python2
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public |
Avro is a serialization and RPC framework.
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2023-06-16 |
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ecopy
|
public |
EcoPy: Ecological Data Analysis in Python
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2023-06-16 |
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minimock
|
public |
The simplest possible mock library
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2023-06-16 |
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r-rentrez
|
public |
Provides an R interface to the NCBI's EUtils API allowing users to search databases
like GenBank and PubMed, process the results of those searches and pull data into
their R sessions.
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2023-06-16 |
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perl-data-dump
|
public |
Pretty printing of data structures
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2023-06-16 |
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epic
|
public |
Chip-Seq broad peak/domain finder.
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2023-06-16 |
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r-flexmix
|
public |
A general framework for finite mixtures of regression models using the EM algorithm is implemented. The package provides the E-step and all data handling, while the M-step can be supplied by the user to easily define new models. Existing drivers implement mixtures of standard linear models, generalized linear models and model-based clustering.
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2023-06-16 |
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perl-test-trap
|
public |
Trap exit codes, exceptions, output, etc.
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2023-06-16 |
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r-mlgt
|
public |
Processing and analysis of high throughput (Roche 454) sequences generated from multiple loci and multiple biological samples. Sequences are assigned to their locus and sample of origin, aligned and trimmed. Where possible, genotypes are called and variants mapped to known alleles.
|
2023-06-16 |
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r-gpseq
|
public |
Some functions for modeling sequence read counts as a generalized poisson model and to use this model for detecting differentially expressed genes in different conditions and differentially spliced exons.
|
2023-06-16 |
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singlecell-barcodes
|
public |
whitelisted singlecell barcodes and information regarding where molecular/sample/cellular barcodes are in each read, for various singlecell protocols
|
2023-06-16 |
|
csb
|
public |
Computational Structural Biology Toolbox
|
2023-06-16 |
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r-openxlsx
|
public |
Simplifies the creation of Excel .xlsx files by providing a high level interface to writing, styling and editing worksheets. Through the use of 'Rcpp', read/write times are comparable to the 'xlsx' and 'XLConnect' packages with the added benefit of removing the dependency on Java.
|
2023-06-16 |
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metametamerge
|
public |
Merging module of the MetaMeta Pipeline
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2023-06-16 |
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r-rcpptoml
|
public |
The configuration format defined by 'TOML' (which expands to "Tom's Obvious Markup Language") specifies an excellent format (described at <https
|
2023-06-16 |
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gff3toembl
|
public |
Submitting annotated genomes to EMBL is a very difficult and time consuming process. This software converts GFF3 files from the most commonly use prokaryote annotation tool Prokka into a format that is suitable for submission to EMBL. It has been used to prepare more than 30% of all annotated genomes in EMBL/GenBank.
|
2023-06-16 |
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nanosplit
|
public |
Perform splitting of Oxford Nanopore sequencing data in a fail and pass dataset.
|
2023-06-16 |
|
gqt
|
public |
GQT is a genotype query interface.
|
2023-06-16 |
|
panoct
|
public |
PanOCT, Pan-genome Ortholog Clustering Tool, is a program for pan-genomic analysis of closely related prokaryotic species or strains
|
2023-06-16 |
|
je-suite
|
public |
Je is a suite to handle barcoded fastq files with (or without) Unique Molecule Identifiers (UMIs) and filter
read duplicates using these UMIs
|
2023-06-16 |
|
jaffa
|
public |
JAFFA is a multi-step pipeline that takes either raw RNA-Seq reads, or pre-assembled transcripts then searches
for gene fusions. This package contains the wrappers jaffa-direct, jaffa-assembly, and jaffa-hybrid.
You can pass the "refSeq" parameter in the environment variables JAFFA_REF_BASE. Otherwise, pass any paramters
to the wrappers as you would to the bpipe JAFFA_{method} call in the manual.
|
2023-06-16 |
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odose
|
public |
Ortholog Direction of Selection Engine.
|
2023-06-16 |
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r-matlab
|
public |
Emulate MATLAB code using R.
|
2023-06-16 |
|
garnet
|
public |
UNKNOWN
|
2023-06-16 |
|
apoc
|
public |
Large-scale structural comparison of protein pockets
|
2023-06-16 |
|
perl-bio-eutilities
|
public |
Webagent which interacts with and retrieves data from NCBI eUtils.
|
2023-06-16 |
|
pyexcelerator
|
public |
generating Excel 97+ files; importing Excel 95+ files; Excel files dumper; OLE2 files dumper; xls2txt, xls2csv, xls2html
|
2023-06-16 |
