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treekin
|
public |
Compute folding dynamics on coarse grained version of an energy landscape by numeric integration of a Markov process
|
2023-06-16 |
|
perl-moosex-clone
|
public |
Fine-grained cloning support for Moose objects.
|
2023-06-16 |
|
bioconductor-copywriter
|
public |
Copy number information from targeted sequencing using off-target reads
|
2023-06-16 |
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bioconductor-biosvd
|
public |
Package for high-throughput data processing, outlier detection, noise removal and dynamic modeling
|
2023-06-16 |
|
perl-file-remove
|
public |
Remove files and directories
|
2023-06-16 |
|
bioconductor-browservizdemo
|
public |
A BrowserViz subclassing example, xy plotting in the browser using d3.
|
2023-06-16 |
|
perl-filedirutil
|
public |
A Moose Role for basic File IO
|
2023-06-16 |
|
perl-ppi
|
public |
Parse, Analyze and Manipulate Perl (without perl)
|
2023-06-16 |
|
perl-tie-refhash-weak
|
public |
A Tie::RefHash subclass with weakened references in the keys.
|
2023-06-16 |
|
perl-tie-refhash
|
public |
use references as hash keys
|
2023-06-16 |
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bioconductor-doqtl
|
public |
DOQTL is a quantitative trait locus (QTL) mapping pipeline designed for Diversity Outbred mice and other multi-parent outbred populations. The package reads in data from genotyping arrays and perform haplotype reconstruction using a hidden Markov model (HMM). The haplotype probabilities from the HMM are then used to perform linkage mapping. When founder sequences are available, DOQTL can use the haplotype reconstructions to impute the founder sequences onto DO genomes and perform association mapping.
|
2023-06-16 |
|
bioconductor-edda
|
public |
Experimental Design in Differential Abundance analysis
|
2023-06-16 |
|
perl-params-coerce
|
public |
Allows your classes to do coercion of parameters
|
2023-06-16 |
|
perl-hook-lexwrap
|
public |
Lexically scoped subroutine wrappers
|
2023-06-16 |
|
perl-tie-toobject
|
public |
Tie to an existing object.
|
2023-06-16 |
|
perl-module-extract-use
|
public |
Pull out the modules a module explicitly uses
|
2023-06-16 |
|
perl-test-object
|
public |
Thoroughly testing objects via registered handlers
|
2023-06-16 |
|
perl-mime-base64
|
public |
The RFC 2045 encodings; base64 and quoted-printable
|
2023-06-16 |
|
perl-data-visitor
|
public |
Visitor style traversal of Perl data structures
|
2023-06-16 |
|
perl-file-share
|
public |
Extend File::ShareDir to Local Libraries
|
2023-06-16 |
|
perl-ipc-cmd
|
public |
A cross platform way of running (interactive) commandline programs.
|
2023-06-16 |
|
ncfp
|
public |
A program/module to find nt sequences that code for aa sequences
|
2023-06-16 |
|
perl-test-file-contents
|
public |
Test routines for examining the contents of files
|
2023-06-16 |
|
perl-test-prereq
|
public |
check if Makefile.PL has the right pre-requisites
|
2023-06-16 |
|
perl-hash-util-fieldhash-compat
|
public |
Use Hash::Util::FieldHash or ties, depending on availability
|
2023-06-16 |
|
bis-snp
|
public |
Bisulfite-seq/NOMe-seq SNPs & cytosine methylation caller
|
2023-06-16 |
|
perl-test-subcalls
|
public |
Track the number of times subs are called
|
2023-06-16 |
|
mvp
|
public |
detect creation/destruction of sequence motifs as a result of mutations
|
2023-06-16 |
|
bioconductor-tdaracne
|
public |
Network reverse engineering from time course data.
|
2023-06-16 |
|
funnel
|
public |
Funnel is a toolkit for distributed task execution via a simple, standard API
|
2023-06-16 |
|
refseq_masher
|
public |
refseq_masher finds what NCBI RefSeq genomes match or are contained within your sequence data using Mash
|
2023-06-16 |
|
tinysink
|
public |
Synchronise Nanopore reads with a server.
|
2023-06-16 |
|
nucamino
|
public |
A nucleotide to amino acid alignment program optimized for virus gene sequences
|
2023-06-16 |
|
r-canopy
|
public |
A statistical framework and computational procedure for identifying the sub-populations within a tumor, determining the mutation profiles of each subpopulation, and inferring the tumor's phylogenetic history. The input are variant allele frequencies (VAFs) of somatic single nucleotide alterations (SNAs) along with allele-specific coverage ratios between the tumor and matched normal sample for somatic copy number alterations (CNAs). These quantities can be directly taken from the output of existing software. Canopy provides a general mathematical framework for pooling data across samples and sites to infer the underlying parameters. For SNAs that fall within CNA regions, Canopy infers their temporal ordering and resolves their phase. When there are multiple evolutionary configurations consistent with the data, Canopy outputs all configurations along with their confidence assessment.
|
2023-06-16 |
|
perl-extutils-pkgconfig
|
public |
simplistic interface to pkg-config
|
2023-06-16 |
|
perl-extutils-depends
|
public |
Easily build XS extensions that depend on XS extensions
|
2023-06-16 |
|
bioconductor-pbcmc
|
public |
The pbcmc package characterizes uncertainty assessment on gene expression classifiers, a. k. a. molecular signatures, based on a permutation test. In order to achieve this goal, synthetic simulated subjects are obtained by permutations of gene labels. Then, each synthetic subject is tested against the corresponding subtype classifier to build the null distribution. Thus, classification confidence measurement can be provided for each subject, to assist physician therapy choice. At present, it is only available for PAM50 implementation in genefu package but it can easily be extend to other molecular signatures.
|
2023-06-16 |
|
nucdiff
|
public |
NucDiff locates and categorizes differences between two closely related nucleotide sequences.
|
2023-06-16 |
|
perl-cairo
|
public |
Perl interface to the cairo 2d vector graphics library
|
2023-06-16 |
|
treemaker
|
public |
A python tool for generating a Newick formatted tree from alist of classifications
|
2023-06-16 |
|
bis-snp-utils
|
public |
bis-snp-utils are support tools for Bis-SNP
|
2023-06-16 |
|
rebaler
|
public |
Reference-based long read assemblies of bacterial genomes
|
2023-06-16 |
|
riboseq-rust
|
public |
Ribo-seq Unit Step Transformation. Tools to characterise the determinants of ribosome profiling read density across mRNA. May be used to examine relative decoding rates and and for quality assessment
|
2023-06-16 |
|
perl-moosex-types-path-tiny
|
public |
MooseX::Types::Path::Tiny - Path::Tiny types and coercions for Moose
|
2023-06-16 |
|
umitools
|
public |
A toolset for handling sequencing data with unique molecular identifiers (UMIs)
|
2023-06-16 |
|
perl-moosex-nonmoose
|
public |
MooseX::NonMoose - easy subclassing of non-Moose classes
|
2023-06-16 |
|
sierrapy
|
public |
A Client of HIVdb Sierra GraphQL Webservice.
|
2023-06-16 |
|
readseq
|
public |
Read & reformat biosequences, Java command-line version
|
2023-06-16 |
|
r-adegenet
|
public |
Toolset for the exploration of genetic and genomic data. Adegenet provides formal (S4) classes for storing and handling various genetic data, including genetic markers with varying ploidy and hierarchical population structure ('genind' class), alleles counts by populations ('genpop'), and genome-wide SNP data ('genlight'). It also implements original multivariate methods (DAPC, sPCA), graphics, statistical tests, simulation tools, distance and similarity measures, and several spatial methods. A range of both empirical and simulated datasets is also provided to illustrate various methods.
|
2023-06-16 |
|
xtail
|
public |
Genome-wide assessment of differential translations with ribosome profiling data
|
2023-06-16 |
