|
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 |
|
snmf
|
public |
Fast and efficient program for estimating individual admixture coefficients based on sparse non-negative matrix factorization and population genetics
|
2023-06-16 |
|
clove
|
public |
CLOVE: Classification of genomic fusions into structural variation events.
|
2023-06-16 |
|
biolite
|
public |
A lightweight bioinformatics framework with automated tracking of diagnostics and provenance.
|
2023-06-16 |
|
hts-nim-tools
|
public |
useful command-line tools written to show-case hts-nim
|
2023-06-16 |
|
anndata
|
public |
An annotated data matrix.
|
2023-06-16 |
|
bioconductor-dchiprep
|
public |
DChIPRep - Analysis of chromatin modification ChIP-Seq data with replication
|
2023-06-16 |
|
bioconductor-onassis
|
public |
OnASSIs Ontology Annotation and Semantic SImilarity software
|
2023-06-16 |
|
rna-cd
|
public |
RNA contamination detector
|
2023-06-16 |
|
fusioncatcher
|
public |
Finder of Somatic Fusion Genes in RNA-seq data.
|
2023-06-16 |
|
prokaryote
|
public |
CellProfiler's Java dependencies
|
2023-06-16 |
|
cocoscore
|
public |
CoCoScore: context-aware co-occurrence scores for biomedical text mining applications
|
2023-06-16 |
|
albatradis
|
public |
Comparative TraDIS analysis
|
2023-06-16 |
|
bioconductor-hmyrib36
|
public |
YRI hapmap + expression (GENEVAR), Build 36, r23a genotypes
|
2023-06-16 |
|
bioconductor-cgdv17
|
public |
Complete Genomics Diversity Panel, chr17 on 46 individuals
|
2023-06-16 |
|
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.
|
2023-06-16 |
|
biopet-sampleconfig
|
public |
#### Tools - ExtractTsv This mean can extract samples, libraries and readgroups from a sample config file.
|
2023-06-16 |
|
perl-bundle-bioperl
|
public |
A bundle to install external CPAN modules used by BioPerl 1.5.2
|
2023-06-16 |
|
bioconductor-pcagopromoter
|
public |
pcaGoPromoter is used to analyze DNA micro array data
|
2023-06-16 |
|
neurodocker
|
public |
Neurodocker is a command-line program that generates custom Dockerfiles and Singularity recipes for neuroimaging and minifies existing containers.
|
2023-06-16 |
|
bioconductor-ceu1kg
|
public |
CEU (N=60) genotypes from 1000 genomes pilot phase I
|
2023-06-16 |
|
bioconductor-junctionseq
|
public |
JunctionSeq: A Utility for Detection of Differential Exon and Splice-Junction Usage in RNA-Seq data
|
2023-06-16 |
|
bioconductor-maxcontrastprojection
|
public |
Perform a maximum contrast projection of 3D images along the z-dimension into 2D
|
2023-06-16 |
|
bioconductor-exomepeak
|
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.
|
2023-06-16 |
|
bioconductor-rsffreader
|
public |
rSFFreader reads sequence, qualities and clip point values from sff files generated by Roche 454 and Life Sciences Ion Torrent sequencers into similar classes as are present for fastq files.
|
2023-06-16 |
|
bioconductor-alsace
|
public |
ALS for the Automatic Chemical Exploration of mixtures
|
2023-06-16 |
|
bioconductor-ceuhm3
|
public |
ceuhm3: genotype (HapMap phase III) and expression data for CEPH CEU cohort
|
2023-06-16 |
|
perl-test-fork
|
public |
test code which forks
|
2023-06-16 |
|
biopet-validatevcf
|
public |
ValidateVcf validates a VCF file against a reference genomes.
|
2023-06-16 |
|
biopet-vcffilter
|
public |
This tool enables a user to filter VCF files.
|
2023-06-16 |
|
perl-ipc-run3
|
public |
run a subprocess with input/ouput redirection
|
2023-06-16 |
|
biopet-seattleseqkit
|
public |
#### Tool - Filter This tool can filter a seattle seq file.
|
2023-06-16 |
|
pbalign
|
public |
Python wrapper for producing PBBAM valid alignments
|
2023-06-16 |
|
perl-test-without-module
|
public |
Test fallback behaviour in absence of modules
|
2023-06-16 |
|
pymisc-utils
|
public |
Utility library for rp-bp
|
2023-06-16 |
|
perl-devel-overloadinfo
|
public |
introspect overloaded operators
|
2023-06-16 |
|
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.
|
2023-06-16 |
|
portcullis
|
public |
Splice junction analysis and filtering from BAM files
|
2023-06-16 |
|
ucsc-endsinlf
|
public |
Check that last letter in files is end of line
|
2023-06-16 |
|
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.
|
2023-06-16 |
|
r-zerone
|
public |
Zerone discretizes several ChIP-seq replicates simultaneously and resolves conflicts between them.
|
2023-06-16 |
|
deblur
|
public |
Deblur is a greedy deconvolution algorithm based on known read error profiles.
|
2023-06-16 |
|
taeper
|
public |
Simulate repeating a nanopore experiment.
|
2023-06-16 |
|
bam2fastx
|
public |
Converting and demultiplexing of PacBio BAM files into gzipped fasta and fastq files
|
2023-06-16 |
|
feelnc
|
public |
FlExible Extraction of LncRNA
|
2023-06-16 |
|
fast5seek
|
public |
Get paths for fast5 files contained in BAM, SAM, or fastq.
|
2023-06-16 |
|
samclip
|
public |
Filter SAM file for soft and hard clipped alignments
|
2023-06-16 |
|
ctat-metagenomics
|
public |
ctat-metagenomics uses centrifuge
|
2023-06-16 |
|
bioconductor-flowq
|
public |
Provides quality control and quality assessment tools for flow cytometry data.
|
2023-06-16 |
