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r-phytools
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public |
Phylogenetic tools for comparative biology
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2023-06-16 |
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vcfsamplecompare
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public |
This script sorts and (optionally) filters the rows/variants of a VCF file (containing data for 2 or more samples) based on the differences in the variant data between samples or sample groups. Degree of "difference" is determined by either the best possible degree of separation of sample groups by genotype calls or the difference in average allelic frequency of each sample or sample group (with a gap size threshold). The pair of samples or sample groups used to represent the difference for a variant row is the one leading to the greatest difference in consistent genotype or average allelic frequencies (i.e. observation ratios, e.g. AO/DP) of the same variant state. If sample groups are not specified, the pair of samples leading to the greatest difference is greedily discovered and chosen to represent the variant/row.
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2023-06-16 |
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bioconductor-genrank
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public |
Candidate gene prioritization based on convergent evidence
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2023-06-16 |
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bioconductor-dexus
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public |
DEXUS - Identifying Differential Expression in RNA-Seq Studies with Unknown Conditions or without Replicates
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2023-06-16 |
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bioconductor-chipxpressdata
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public |
ChIPXpress Pre-built Databases
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2023-06-16 |
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dca
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public |
Count autoencoder for scRNA-seq denoising
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2023-06-16 |
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bioconductor-encodexplorer
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public |
A compilation of ENCODE metadata
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2023-06-16 |
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gemma
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public |
Linear mixed models (LMMs) for genome-wide association (GWA)
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2023-06-16 |
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pb-assembly
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public |
Meta-package for Falcon/Unzip tool-suite (originally by Jason Chin)
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2023-06-16 |
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taxator-tk
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public |
Taxator-tk sequence taxonomic annotaion
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2023-06-16 |
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r-seqminer
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public |
Integrate sequencing data (Variant call format, e.g. VCF or BCF) or meta-analysis results in R. This package can help you (1) read VCF/BCF files by chromosomal ranges (e.g. 1:100-200); (2) read RareMETAL summary statistics files; (3) read tables from a tabix-indexed files; (4) annotate VCF/BCF files; (5) create customized workflow based on Makefile.
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2023-06-16 |
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r-rnexml
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public |
Provides access to phyloinformatic data in 'NeXML' format. The package should add new functionality to R such as the possibility to manipulate 'NeXML' objects in more various and refined way and compatibility with 'ape' objects.
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2023-06-16 |
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riborex
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public |
Riborex is a R package for identification of differential translation from Ribo-seq data.
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2023-06-16 |
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kopt
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public |
Keras-hyperopt (kopt); Hyper-parameter tuning for Keras using hyperopt.
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2023-06-16 |
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octopus
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public |
Octopus is a mapping-based variant caller that implements several calling models within a unified haplotype-aware framework.
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2023-06-16 |
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bazam
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public |
A tool to extract paired reads in FASTQ format from coordinate sorted BAM files
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2023-06-16 |
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lexmapr
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public |
A Lexicon and Rule-Based Tool for Translating Short Biomedical Specimen Descriptions into Semantic Web Ontology Terms
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2023-06-16 |
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perl-bio-automatedannotation
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public |
Automated annotation of assemblies
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2023-06-16 |
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tinyfasta
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public |
Tiny Python package, with no external dependencies, for parsing FASTA sequence files.
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2023-06-16 |
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perl-gtdbtk
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public |
Perl script and dependent library files required for GTDB-Tk.
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2023-06-16 |
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kinsimriboswitch
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public |
Pipeline for the simulation of RNA--ligand interaction kinetics as
outlined in Kuehnl et al. 2017, https://doi.org/10.1186/s12859-017-1823-5
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2023-06-16 |
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reparation_blast
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public |
A pipeline that detects novel open reading frames with ribseq data for bacteria.
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2023-06-16 |
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r-popgenome
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public |
Provides efficient tools for population genomics data analysis, able to process individual loci, large sets of loci, or whole genomes. PopGenome <DOI:10.1093/molbev/msu136> not only implements a wide range of population genetics statistics, but also facilitates the easy implementation of new algorithms by other researchers. PopGenome is optimized for speed via the seamless integration of C code.
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2023-06-16 |
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slamdunk
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public |
Slamdunk is a software tool for SLAMseq data analysis.
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2023-06-16 |
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biolib
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public |
Package for common tasks in bioinformatics.
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2023-06-16 |
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revtrans
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public |
revtrans - performs a reverse translation of a peptide alignment.
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2023-06-16 |
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r-blockfest
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public |
An R implementation of an extension of the 'BayeScan' software (Foll, 2008) <DOI:10.1534/genetics.108.092221> for codominant markers, adding the option to group individual SNPs into pre-defined blocks. A typical application of this new approach is the identification of genomic regions, genes, or gene sets containing one or more SNPs that evolved under directional selection.
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2023-06-16 |
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flowcraft
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public |
A Nextflow pipeline assembler for genomics. Pick your modules. Assemble them. Run the pipeline.
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2023-06-16 |
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duphold
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public |
SV callers like lumpy look at split-reads and pair distances to find structural variants. This tool is a fast way to add depth information to those calls.
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2023-06-16 |
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gatktool
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public |
Functions and classes used to extend a GATK tool with Python
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2023-06-16 |
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r-metstat
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public |
A diverse collection of metabolomics related statistical tools.
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2023-06-16 |
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admixture
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public |
ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets.
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2023-06-16 |
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perl-autodie
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public |
Replace functions with ones that succeed or die with lexical scope
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2023-06-16 |
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bufet
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public |
Tool that performs the unbiased miRNA functional enrichment analysis (Bleazard et al.) requiring significantly reduced excution times (less than 10 minutes for 1 million iterations).
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2023-06-16 |
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smeg
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public |
Strain-level Metagenomic Estimation of Growth rate (SMEG) measures growth rates of microbial strains from complex metagenomic dataset
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2023-06-16 |
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dadi
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public |
Fit population genetic models using diffusion approximations to the allele frequency spectrum
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2023-06-16 |
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rpf-count-cds
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public |
A python script for counting RPF reads map to CDS region.
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2023-06-16 |
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scvi
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public |
Single-cell Variational Inference
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2023-06-16 |
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perl-snap
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public |
SNAP calculates pairwise synonymous and nonsynonymous distances according to the Nei and Gojobori method for an alignment in table format.
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2023-06-16 |
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phame
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public |
A tool to derive SNP matrices and phylogenetic tree from raw reads, contigs, and full genomes.
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2023-06-16 |
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delegation
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public |
Simple implementation of the delegate pattern.
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2023-06-16 |
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mccortex
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public |
De novo genome assembly and multisample variant calling
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2023-06-16 |
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libarbdb
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public |
ARB 6 Sequence Analysis Suite
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2023-06-16 |
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genclust
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public |
A genetic algorithm for clustering gene expression data.
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2023-06-16 |
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arb-bio-tools
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public |
ARB 6 Sequence Analysis Suite
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2023-06-16 |
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arb-bio-devel
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public |
ARB 6 Sequence Analysis Suite
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2023-06-16 |
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python-rnacentral
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public |
This tool exploits the RNAcentral public APIs to automatically retrieve sequences (converted to the FASTA format) and the related metadata, starting with one or a list of RNAcentral IDs
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2023-06-16 |
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smcounter2
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public |
smCounter2: an accurate low-frequency variant caller for targeted sequencing data with unique molecular identifiers
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2023-06-16 |
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ghost-tree
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public |
ghost-tree is a bioinformatics tool that combines sequence data from two
genetic marker databases into one phylogenetic tree that can be used for
diversity analyses.
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2023-06-16 |
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shannon
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public |
A program for assembling transcripts from RNA-Seq data.
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2023-06-16 |
