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cactus
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public |
Cactus is a reference-free whole-genome multiple alignment program based upon notion of Cactus graphs
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2023-06-16 |
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bioconductor-rchyoptimyx
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public |
Optimyzed Cellular Hierarchies for Flow Cytometry
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2023-06-16 |
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bioconductor-flowtype
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public |
Phenotyping Flow Cytometry Assays
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2023-06-16 |
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bioconductor-ampliqueso
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public |
The package provides tools and reports for the analysis of amplicon sequencing panels, such as AmpliSeq
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2023-06-16 |
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r-disco
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public |
Concordance and discordance of homologous gene regulation allows comparing reaction to stimuli in different organisms, for example human patients and animal models of a disease. The package contains functions to calculate discordance and concordance score for homologous gene pairs, identify concordantly or discordantly regulated transcriptional modules and visualize the results. It is intended for analysis of transcriptional data.
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2023-06-16 |
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halla
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public |
HAllA: Hierarchically All-against-All Association Testing.
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2023-06-16 |
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scater-scripts
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public |
A set of wrappers for individual components of the Scater package. Functions R packages are hard to call when building workflows outside of R, so this package adds a set of simple wrappers with robust argument parsing. Intermediate steps are currently mainly serialized R objects, but the ultimate objective is to have language-agnostic intermediate formats allowing composite workflows using a variety of software packages.
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2023-06-16 |
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oncotator
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public |
Oncotator is a tool for annotating human genomic point mutations and indels with data relevant to cancer researchers.
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2023-06-16 |
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ncbi-util-legacy
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public |
NCBI software development toolkit
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2023-06-16 |
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biobb_wf_mutations
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public |
Lysozyme plus Mutations workflow built using BioBB Based on the official Gromacs tutorial: http://www.mdtutorials.com/gmx/lysozyme/01_pdb2gmx.html
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2023-06-16 |
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mantis
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public |
Mantis: A Fast, Small, and Exact Large-Scale Sequence-Search Index
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2023-06-16 |
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biobb_adapters
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public |
Biobb_adapters is the Biobb module collection to use the building blocks with several workflow managers.
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2023-06-16 |
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jobtree
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public |
Python based pipeline management software for clusters that makes running recursive and dynamically scheduled computations straightforward
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2023-06-16 |
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bigsi
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public |
BItsliced Genomic Signature Index [BIGSI]
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2023-06-16 |
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spotyping3
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public |
SpoTyping3: fast and accurate in silico Mycobacterium spoligotyping from sequence reads, compatible with Python3
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2023-06-16 |
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mirfix
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public |
MIRfix automatically curates miRNA datasets by improving alignments of their precursors, the consistency of the annotation of mature miR and miR* sequence, and the phylogenetic coverage. MIRfix produces alignments that are comparable across families and sets the stage for improved homology search as well as quantitative analyses.
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2023-06-16 |
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rawtools
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public |
RawTools is an open-source and freely available package designed to perform scan data parsing and quantification, and quality control analysis of Thermo Orbitrap raw mass spectrometer files.
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2023-06-16 |
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panphlan
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public |
PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition and *in-vivo* transcriptional activity of individual strains in metagenomic samples.
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2023-06-16 |
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clairvoyante
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public |
Identifying the variants of DNA sequences sensitively and accurately is an important but challenging task in the field of genomics. This task is particularly difficult when dealing with Single Molecule Sequencing, the error rate of which is still tens to hundreds of times higher than Next Generation Sequencing. With the increasing prevalence of Single Molecule Sequencing, an efficient variant caller will not only expedite basic research but also enable various downstream applications. To meet this demand, we developed Clairvoyante, a multi-task five-layer convolutional neural network model for predicting variant type, zygosity, alternative allele and Indel length. On NA12878, Clairvoyante achieved 99.73%, 97.68% and 95.36% accuracy on known variants, and achieved 98.65%, 92.57%, 77.89% F1 score on the whole genome, in Illumina, PacBio, and Oxford Nanopore data, respectively. Training Clairvoyante with a sample and call variant on another shows that Clairvoyante is sample agnostic and general for variant calling. A slim version of Clairvoyante with reduced model parameters produced a much lower F1, suggesting the full model's power in disentangling subtle details in read alignment. Clairvoyante is the first method for Single Molecule Sequencing to finish a whole genome variant calling in two hours on a 28 CPU-core machine, with top-tier accuracy and sensitivity. A toolset was developed to train, utilize and visualize the Clairvoyante model easily, and is publically available here is this repo.
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2023-06-16 |
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sc3-scripts
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public |
A set of wrappers for individual components of the SC3 package. Functions R packages are hard to call when building workflows outside of R, so this package adds a set of simple wrappers with robust argument parsing. Intermediate steps are currently mainly serialized R objects, but the ultimate objective is to have language-agnostic intermediate formats allowing composite workflows using a variety of software packages.
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2023-06-16 |
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pytest-workflow
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public |
A pytest plugin for configuring workflow/pipeline tests using YAML files
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2023-06-16 |
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spectrum_utils
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public |
Mass spectrometry utility functions
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2023-06-16 |
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r-transformer
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public |
Additional S3 and S4 coercion methods for easy interconversion between Bioconductor and tidyverse data classes.
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2023-06-16 |
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r-ldrtools
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public |
Linear dimension reduction subspaces can be uniquely defined using orthogonal projection matrices. This package provides tools to compute distances between such subspaces and to compute the average subspace. For details see Liski, E.Nordhausen K., Oja H., Ruiz-Gazen A. (2016) Combining Linear Dimension Reduction Subspaces <doi:10.1007/978-81-322-3643-6_7>.
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2023-06-16 |
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bioconductor-sc3-scripts
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public |
A set of wrappers for individual components of the SC3 package. Functions R packages are hard to call when building workflows outside of R, so this package adds a set of simple wrappers with robust argument parsing. Intermediate steps are currently mainly serialized R objects, but the ultimate objective is to have language-agnostic intermediate formats allowing composite workflows using a variety of software packages.
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2023-06-16 |
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gff3sort
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public |
A Perl Script to sort gff3 files and produce suitable results for tabix tools
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2023-06-16 |
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bioconductor-idmappinganalysis
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public |
ID Mapping Analysis
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2023-06-16 |
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bioconductor-msgfgui
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public |
A shiny GUI for MSGFplus
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2023-06-16 |
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bioconductor-envisionquery
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public |
Retrieval from the ENVISION bioinformatics data portal into R
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2023-06-16 |
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bioconductor-compgo
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public |
An R pipeline for .bed file annotation, comparing GO term enrichment between gene sets and data visualisation
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2023-06-16 |
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ucsc-hggoldgapgl
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public |
Put chromosome .agp and .gl files into browser database.
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2023-06-16 |
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barcode_splitter
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public |
Split multiple fastq files by matching barcodes in one or more of the sequence files. Barcodes in the tab-delimited barcodes.txt file are matched against the beginning (or end) of the specified index read(s). By default, barcodes must match exactly, but --mistmatches can be set higher if desired. Compressed input is read (from all files) if the first input file name ends in .gz. Reading of compressed input can be forced with the gzipin option.
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2023-06-16 |
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pylprotpredictor
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public |
A tool to predict PYL proteins
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2023-06-16 |
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shapeshifter-cli
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public |
A command-line tool for transforming large data sets
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2023-06-16 |
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bioconductor-msgfplus
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public |
An interface between R and MS-GF+
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2023-06-16 |
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abeona
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public |
A simple transcriptome assembler based on kallisto and Cortex graphs.
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2023-06-16 |
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bioconductor-flowqb
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public |
flowQB is a fully automated R Bioconductor package to calculate automatically the detector efficiency (Q), optical background (B) and intrinsic CV of the beads.
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2023-06-16 |
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bioconductor-idmappingretrieval
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public |
ID Mapping Data Retrieval
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2023-06-16 |
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perl-data-match
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public |
Complex data structure pattern matching
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2023-06-16 |
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mtb-snp-it
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public |
SNP-IT: Whole genome SNP based identification of members of the Mycobacterium tuberculosis complex.
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2023-06-16 |
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r-ampliconduo
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public |
Increasingly powerful techniques for high-throughput sequencing open the possibility to comprehensively characterize microbial communities, including rare species. However, a still unresolved issue are the substantial error rates in the experimental process generating these sequences. To overcome these limitations we propose an approach, where each sample is split and the same amplification and sequencing protocol is applied to both halves. This procedure should allow to detect likely PCR and sequencing artifacts, and true rare species by comparison of the results of both parts. The AmpliconDuo package, whereas amplicon duo from here on refers to the two amplicon data sets of a split sample, is intended to help interpret the obtained read frequency distribution across split samples, and to filter the false positive reads.
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2023-06-16 |
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bioconductor-rdavidwebservice
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public |
An R Package for retrieving data from DAVID into R objects using Web Services API.
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2023-06-16 |
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perl-string-escape
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public |
Backslash escapes, quoted phrase, word elision, etc.
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2023-06-16 |
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perl-data-compare
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public |
compare perl data structures
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2023-06-16 |
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ucsc-hgvstovcf
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public |
Convert HGVS terms to VCF tab-separated output
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2023-06-16 |
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spydrpick
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public |
Mutual information based detection of pairs of genomic loci co-evolving under a shared selective pressure
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2023-06-16 |
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apollo
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public |
WebApollo API library
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2023-06-16 |
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bioconductor-camthc
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public |
Convex Analysis of Mixtures for Tissue Heterogeneity Characterization
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2023-06-16 |
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tango
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public |
Assign taxonomy to metagenomic contigs
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2023-06-16 |
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ucsc-chainbridge
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public |
Attempt to extend alignments through double-sided gaps of similar size
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2023-06-16 |
