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savage
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public |
SAVAGE (Strain Aware VirAl GEnome assembly) reconstructs individual (viral) haplotypes from a mixed sample.
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2023-06-16 |
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r-r2html
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public |
Includes HTML function and methods to write in an HTML file. Thus, making HTML reports is easy. Includes a function that allows redirection on the fly, which appears to be very useful for teaching purpose, as the student can keep a copy of the produced output to keep all that he did during the course. Package comes with a vignette describing how to write HTML reports for statistical analysis. Finally, a driver for 'Sweave' allows to parse HTML flat files containing R code and to automatically write the corresponding outputs (tables and graphs).
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2023-06-16 |
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r-ggalt
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public |
A compendium of new geometries, coordinate systems, statistical transformations, scales and fonts for 'ggplot2', including splines, 1d and 2d densities, univariate average shifted histograms, a new map coordinate system based on the 'PROJ.4'-library along with geom_cartogram() that mimics the original functionality of geom_map(), formatters for "bytes", a stat_stepribbon() function, increased 'plotly' compatibility and the 'StateFace' open source font 'ProPublica'. Further new functionality includes lollipop charts, dumbbell charts, the ability to encircle points and coordinate-system-based text annotations.
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2023-06-16 |
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avro-python3
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public |
Avro is a serialization and RPC framework.
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2023-06-16 |
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hlaprofiler
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public |
HLAProfiler uses k-mer profiles to predict HLA types from paired-end RNA-seq data.
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2023-06-16 |
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r-reshape
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public |
Flexibly restructure and aggregate data using just melt() and cast().
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2023-06-16 |
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r-kernlab
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public |
Kernel-based machine learning methods for classification, regression, clustering, novelty detection, quantile regression and dimensionality reduction. Among other methods 'kernlab' includes Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes and a QP solver.
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2023-06-16 |
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pysvg
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public |
Python SVG Library
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2023-06-16 |
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outrigger
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public |
Outrigger detects *de novo* exons and quantifies their percent spliced-in
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2023-06-16 |
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perl-tie-log4perl
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public |
Tie a filehandle to log via Log4perl
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2023-06-16 |
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rnftools
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public |
RNF framework for NGS: simulation of reads, evaluation of mappers, conversion of RNF-compliant data.
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2023-06-16 |
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trawler
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public |
Trawler is a motif discovery tool used to identify enriched motifs in a set of sequenced regions of DNA.
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2023-06-16 |
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scg
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public |
The single cell genotyper (SCG): "Roth A, McPherson A, Laks E, Biele J, Yap D, Wan A, et al. Clonal genotype and population structure inference from single-cell tumor sequencing. Nat Meth. 2016;13: 573–576. doi:10.1038/nmeth.3867"
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2023-06-16 |
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r-cnogpro
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public |
Methods for assigning copy number states and breakpoints in resequencing experiments of prokaryotic organisms.
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2023-06-16 |
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kraken-ea
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public |
Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. This is a modified version allowing for splitting of fastq files based on read classifications.
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2023-06-16 |
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xxhash
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public |
Python binding for xxHash
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2023-06-16 |
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xdg
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public |
Variables defined by the XDG Base Directory Specification
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2023-06-16 |
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nglview
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public |
An IPython widget to interactively view molecular structures and trajectories. Utilizes the embeddable NGL Viewer for rendering.
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2023-06-16 |
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variantbam
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public |
Filtering and profiling of next-generational sequencing data using region-specific rules
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2023-06-16 |
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w4mclstrpeakpics
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public |
Visualize W4M sample-cluster peaks - Produce a figure to assess the similarities and differences among peaks in a cluster of samples using XCMS-preprocessed data files as input. MIT Licence allows redistribution.
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2023-06-16 |
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minialign
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public |
Fast and accurate alignment tool for PacBio and Nanopore long reads.
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2023-06-16 |
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r-rematch2
|
public |
Wrappers on 'regexpr' and 'gregexpr' to return the match results in tidy data frames.
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2023-06-16 |
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perl-file-temp
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public |
No Summary
|
2023-06-16 |
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nanoraw
|
public |
Analysis of nanopore sequencing data.
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2023-06-16 |
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r-microseq
|
public |
Basic functions for microbial sequence data analysis.
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2023-06-16 |
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gdsctools
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public |
Set of tools and pipelines to analyse GDSC data (cancerrxgene.org)
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2023-06-16 |
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lace
|
public |
Building SuperTranscripts: A linear representation of transcriptome data
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2023-06-16 |
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r-minpack.lm
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public |
The nls.lm function provides an R interface to lmder and lmdif from the MINPACK library, for solving nonlinear least-squares problems by a modification of the Levenberg-Marquardt algorithm, with support for lower and upper parameter bounds. The implementation can be used via nls-like calls using the nlsLM function.
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2023-06-16 |
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indelfixer
|
public |
A sensitive aligner for 454, Illumina and PacBio data, employing a full Smith-Waterman alignment against a reference.
|
2023-06-16 |
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perl-constant
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public |
No Summary
|
2023-06-16 |
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perl-pod-coverage-trustpod
|
public |
allow a module's pod to contain Pod::Coverage hints
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2023-06-16 |
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perl-lib
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public |
No Summary
|
2023-06-16 |
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snns
|
public |
No Summary
|
2023-06-16 |
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effectivet3
|
public |
No Summary
|
2023-06-16 |
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ebisearch
|
public |
No Summary
|
2023-06-16 |
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json_collect_data_source
|
public |
This tool is able to receive multiple datasets (optionally with their metadata) in a single query. As an extension of the galaxy-json-data-source tool (https://github.com/mdshw5/galaxy-json-data-source), it allows to handle archives (gz, bz2, tar, and zip) organizing their content in a collection.
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2023-06-16 |
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arb-bio
|
public |
ARB 6 Sequence Analysis Suite
|
2023-06-16 |
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bctools
|
public |
Tools for handling barcodes in NGS data.
|
2023-06-16 |
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perl-pod-parser
|
public |
No Summary
|
2023-06-16 |
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perl-parent
|
public |
No Summary
|
2023-06-16 |
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perl-pod-simple
|
public |
No Summary
|
2023-06-16 |
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perl-pod-escapes
|
public |
No Summary
|
2023-06-16 |
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dxua
|
public |
command-line tool for uploading files to the DNAnexus Platform
|
2023-06-16 |
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perl-test
|
public |
No Summary
|
2023-06-16 |
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crisper_recognition_tool
|
public |
A tool for automatic detection of clustered regularly interspaced palindromic repeats (CRISPR).
|
2023-06-16 |
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r-maxlik
|
public |
Functions for Maximum Likelihood (ML) estimation and non-linear optimization, and related tools. It includes a unified way to call different optimizers, and classes and methods to handle the results from the ML viewpoint. It also includes a number of convenience tools for testing and developing your own models.
|
2023-06-16 |
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represent
|
public |
No Summary
|
2023-06-16 |
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perl-pod-coverage
|
public |
No Summary
|
2023-06-16 |
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perl-test-pod-coverage
|
public |
No Summary
|
2023-06-16 |
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proot
|
public |
No Summary
|
2023-06-16 |
