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nucamino
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public |
A nucleotide to amino acid alignment program optimized for virus gene sequences
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2023-06-16 |
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r-canopy
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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.
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2023-06-16 |
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perl-extutils-pkgconfig
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public |
simplistic interface to pkg-config
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2023-06-16 |
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perl-extutils-depends
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public |
Easily build XS extensions that depend on XS extensions
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2023-06-16 |
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bioconductor-pbcmc
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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.
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2023-06-16 |
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nucdiff
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public |
NucDiff locates and categorizes differences between two closely related nucleotide sequences.
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2023-06-16 |
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perl-cairo
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public |
Perl interface to the cairo 2d vector graphics library
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2023-06-16 |
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treemaker
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public |
A python tool for generating a Newick formatted tree from alist of classifications
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2023-06-16 |
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bis-snp-utils
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public |
bis-snp-utils are support tools for Bis-SNP
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2023-06-16 |
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rebaler
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public |
Reference-based long read assemblies of bacterial genomes
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2023-06-16 |
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riboseq-rust
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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
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2023-06-16 |
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perl-moosex-types-path-tiny
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public |
MooseX::Types::Path::Tiny - Path::Tiny types and coercions for Moose
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2023-06-16 |
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umitools
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public |
A toolset for handling sequencing data with unique molecular identifiers (UMIs)
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2023-06-16 |
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perl-moosex-nonmoose
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public |
MooseX::NonMoose - easy subclassing of non-Moose classes
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2023-06-16 |
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sierrapy
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public |
A Client of HIVdb Sierra GraphQL Webservice.
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2023-06-16 |
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readseq
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public |
Read & reformat biosequences, Java command-line version
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2023-06-16 |
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r-adegenet
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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.
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2023-06-16 |
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xtail
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public |
Genome-wide assessment of differential translations with ribosome profiling data
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2023-06-16 |
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snmf
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public |
Fast and efficient program for estimating individual admixture coefficients based on sparse non-negative matrix factorization and population genetics
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2023-06-16 |
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clove
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public |
CLOVE: Classification of genomic fusions into structural variation events.
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2023-06-16 |
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biolite
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public |
A lightweight bioinformatics framework with automated tracking of diagnostics and provenance.
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2023-06-16 |
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hts-nim-tools
|
public |
useful command-line tools written to show-case hts-nim
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2023-06-16 |
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gmap-fusion
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public |
GMAP-fusion is a utility for identifying candidate fusion transcripts based on transcript sequences reconstructed via RNA-Seq de novo transcriptome assembly.
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2023-06-16 |
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anndata
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public |
An annotated data matrix.
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2023-06-16 |
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bioconductor-dchiprep
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public |
DChIPRep - Analysis of chromatin modification ChIP-Seq data with replication
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2023-06-16 |
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cocoscore
|
public |
CoCoScore: context-aware co-occurrence scores for biomedical text mining applications
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2023-06-16 |
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pheniqs
|
public |
Pheniqs is a flexible generic barcode classifier for high-throughput next-gen sequencing written in multi threaded C++11. It caters to a wide variety of experimental designs by addressing multiple combinatorial index tags in arbitrary locations along reads. Pheniqs implements a noise and quality aware probabilistic classifier with improved accuracy over standard edit distance methods and reports classification quality in standard SAM auxiliary tags. Please not configuation syntax has slightly changed for 2.1.x version.
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2023-06-16 |
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biopet-sampleconfig
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public |
#### Tools - ExtractTsv This mean can extract samples, libraries and readgroups from a sample config file.
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2023-06-16 |
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perl-bundle-bioperl
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public |
A bundle to install external CPAN modules used by BioPerl 1.5.2
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2023-06-16 |
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bioconductor-pcagopromoter
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public |
pcaGoPromoter is used to analyze DNA micro array data
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2023-06-16 |
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neurodocker
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public |
Neurodocker is a command-line program that generates custom Dockerfiles and Singularity recipes for neuroimaging and minifies existing containers.
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2023-06-16 |
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bioconductor-junctionseq
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public |
JunctionSeq: A Utility for Detection of Differential Exon and Splice-Junction Usage in RNA-Seq data
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2023-06-16 |
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bioconductor-exomepeak
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public |
The package is developed for the analysis of affinity-based epitranscriptome shortgun sequencing data from MeRIP-seq (maA-seq). It was built on the basis of the exomePeak MATLAB package (Meng, Jia, et al. "Exome-based analysis for RNA epigenome sequencing data." Bioinformatics 29.12 (2013): 1565-1567.) with new functions for differential analysis of two experimental conditions to unveil the dynamics in post-transcriptional regulation of the RNA methylome. The exomePeak R-package accepts and statistically supports multiple biological replicates, internally removes PCR artifacts and multi-mapping reads, outputs exome-based binding sites (RNA methylation sites) and detects differential post-transcriptional RNA modification sites between two experimental conditions in term of percentage rather the absolute amount. The package is still under active development, and we welcome all biology and computation scientist for all kinds of collaborations and communications. Please feel free to contact Dr. Jia Meng <[email protected]> if you have any questions.
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2023-06-16 |
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perl-test-fork
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public |
test code which forks
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2023-06-16 |
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biopet-validatevcf
|
public |
ValidateVcf validates a VCF file against a reference genomes.
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2023-06-16 |
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biopet-vcffilter
|
public |
This tool enables a user to filter VCF files.
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2023-06-16 |
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perl-ipc-run3
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public |
run a subprocess with input/ouput redirection
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2023-06-16 |
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biopet-seattleseqkit
|
public |
#### Tool - Filter This tool can filter a seattle seq file.
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2023-06-16 |
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pbalign
|
public |
Python wrapper for producing PBBAM valid alignments
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2023-06-16 |
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perl-test-without-module
|
public |
Test fallback behaviour in absence of modules
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2023-06-16 |
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pymisc-utils
|
public |
Utility library for rp-bp
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2023-06-16 |
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perl-devel-overloadinfo
|
public |
introspect overloaded operators
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2023-06-16 |
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r-kinship2
|
public |
Routines to handle family data with a pedigree object. The initial purpose was to create correlation structures that describe family relationships such as kinship and identity-by-descent, which can be used to model family data in mixed effects models, such as in the coxme function. Also includes a tool for pedigree drawing which is focused on producing compact layouts without intervention. Recent additions include utilities to trim the pedigree object with various criteria, and kinship for the X chromosome.
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2023-06-16 |
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portcullis
|
public |
Splice junction analysis and filtering from BAM files
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2023-06-16 |
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ucsc-endsinlf
|
public |
Check that last letter in files is end of line
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2023-06-16 |
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r-quorts
|
public |
The QoRTs software package is a fast, efficient, and portable multifunction toolkit designed to assist in the analysis, quality control, and data management of RNA-Seq datasets.
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2023-06-16 |
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r-zerone
|
public |
Zerone discretizes several ChIP-seq replicates simultaneously and resolves conflicts between them.
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2023-06-16 |
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deblur
|
public |
Deblur is a greedy deconvolution algorithm based on known read error profiles.
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2023-06-16 |
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taeper
|
public |
Simulate repeating a nanopore experiment.
|
2023-06-16 |
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bam2fastx
|
public |
Converting and demultiplexing of PacBio BAM files into gzipped fasta and fastq files
|
2023-06-16 |
