|
mtb-snp-it
|
public |
SNP-IT: Whole genome SNP based identification of members of the Mycobacterium tuberculosis complex.
|
2023-06-16 |
|
r-ampliconduo
|
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.
|
2023-06-16 |
|
bioconductor-rdavidwebservice
|
public |
An R Package for retrieving data from DAVID into R objects using Web Services API.
|
2023-06-16 |
|
perl-string-escape
|
public |
Backslash escapes, quoted phrase, word elision, etc.
|
2023-06-16 |
|
perl-data-compare
|
public |
compare perl data structures
|
2023-06-16 |
|
ucsc-hgvstovcf
|
public |
Convert HGVS terms to VCF tab-separated output
|
2023-06-16 |
|
spydrpick
|
public |
Mutual information based detection of pairs of genomic loci co-evolving under a shared selective pressure
|
2023-06-16 |
|
apollo
|
public |
WebApollo API library
|
2023-06-16 |
|
bioconductor-camthc
|
public |
Convex Analysis of Mixtures for Tissue Heterogeneity Characterization
|
2023-06-16 |
|
tango
|
public |
Assign taxonomy to metagenomic contigs
|
2023-06-16 |
|
ucsc-chainbridge
|
public |
Attempt to extend alignments through double-sided gaps of similar size
|
2023-06-16 |
|
ucsc-clustergenes
|
public |
Cluster genes from genePred tracks
|
2023-06-16 |
|
ucsc-bedjointaboffset
|
public |
given a bed file and tab file where each have a column with matching values: first get the value of column0, the offset and line length from inTabFile. Then go over the bed file, use the name field and append its offset and length to the bed file as two separate fields. Write the new bed file to outBed.
|
2023-06-16 |
|
pbccs
|
public |
pbccs - Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)
|
2023-06-16 |
|
shapeshifter
|
public |
A tool for managing large datasets
|
2023-06-16 |
|
compare-reads
|
public |
cythonized function to compare reads by name.
|
2023-06-16 |
|
socru
|
public |
Order and orientation of complete bacterial genomes
|
2023-06-16 |
|
igor_vdj
|
public |
IGoR is a C++ software designed to infer V(D)J recombination related processes from sequencing data.
|
2023-06-16 |
|
scanpy
|
public |
Single-Cell Analysis in Python. Scales to >1M cells.
|
2023-06-16 |
|
r-momr
|
public |
'MetaOMineR' suite is a set of R packages that offers many functions and modules needed for the analyses of quantitative metagenomics data. 'momr' is the core package and contains routines for biomarker identification and exploration. Developed since the beginning of field, 'momr' has evolved and is structured around the different modules such as preprocessing, analysis, vizualisation, etc. See package help for more information.
|
2023-06-16 |
|
wg-blimp
|
public |
wg-blimp (Whole Genome BisuLfIte sequencing Methylation analysis Pipeline)
|
2023-06-16 |
|
msp2db
|
public |
Python package to create an SQLite database from a collection of MSP mass spectromertry spectra files. Currently works with MSP files formated as MassBank records or as MoNA records. The resulting SQLite database can be used for spectral matching with msPurity Bioconductor R package,
|
2023-06-16 |
|
tximport-scripts
|
public |
A set of wrappers for individual components of the tximport 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.
|
2023-06-16 |
|
r-brio
|
public |
Biological R input/output.
|
2023-06-16 |
|
r-bioverbs
|
public |
S4 generic functions for bioinformatics.
|
2023-06-16 |
|
perl-text-levenshtein
|
public |
calculate the Levenshtein edit distance between two strings
|
2023-06-16 |
|
dammet
|
public |
Software to reconstruct methylomes from HTS data from ancient specimen
|
2023-06-16 |
|
stream_atac
|
public |
STREAM-Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data. Preprocessing steps for single cell atac-seq data.
|
2023-06-16 |
|
artemis
|
public |
A set of Java genome visualization tools including the Artemis genome browser & annotation tool, ACT DNA sequence comparison viewer, DNA Plotter image generation tool and the BamView BAM/CRAM file viewer.
|
2023-06-16 |
|
minnow
|
public |
A principled framework for rapid simulation of dscRNA-seq data at the read level
|
2023-06-16 |
|
imctools
|
public |
An Image Mass Cytometry (IMC) file conversion tool that aims to convert IMC rawfiles (.mcd, .txt) into an intermediary ome.tiff, containing all the relevant metadata. Further it contains tools to generate simpler tiff files that can be directly be used as input files for e.g. CellProfiller, Ilastik, Fiji etc
|
2023-06-16 |
|
srnapipe
|
public |
Pipeline for bioinformatic in-depth exploration of small RNA-seq data
|
2023-06-16 |
|
pypairs
|
public |
A python scRNA-Seq classifier
|
2023-06-16 |
|
perl-html-form
|
public |
Class that represents an HTML form element
|
2023-06-16 |
|
perl-www-mechanize
|
public |
Handy web browsing in a Perl object
|
2023-06-16 |
|
islandpath
|
public |
IslandPath-DIMOB is a standalone software to predict genomic islands in bacterial and archaeal genomes based on the presence of dinucleotide biases and mobility genes.
Genomic islands (GIs) are clusters of genes in prokaryotic genomes of probable horizontal origin. GIs are disproportionately associated with microbial adaptations of medical or environmental interest.
|
2023-06-16 |
|
illumina-cleanup
|
public |
Nextflow pipeline for pre-processing Illumina FASTQ files
|
2023-06-16 |
|
pathogist
|
public |
Calibrated multi-criterion genomic analysis for public health microbiology
|
2023-06-16 |
|
piret
|
public |
A tool for conducting RNA seq analysis.
|
2023-06-16 |
|
gerp
|
public |
GERP identifies constrained elements in multiple alignments by quantifying substitution deficits.
|
2023-06-16 |
|
mofapy
|
public |
Multi-Omics Factor Analysis
|
2023-06-16 |
|
maxquant
|
public |
MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. License restricted.
|
2023-06-16 |
|
biotradis
|
public |
A set of tools to analyse the output from TraDIS analyses
|
2023-06-16 |
|
plantcv
|
public |
An image processing package for plant phenotyping.
|
2023-06-16 |
|
bioconductor-proteoqc
|
public |
An R package for proteomics data quality control
|
2023-06-16 |
|
bioconductor-pga
|
public |
An package for identification of novel peptides by customized database derived from RNA-Seq
|
2023-06-16 |
|
unifrac
|
public |
Fast phylogenetic diversity calculations
|
2023-06-16 |
|
perl-moosex-singleton
|
public |
Turn your Moose class into a singleton
|
2023-06-16 |
|
bioconductor-platecore
|
public |
Provides basic S4 data structures and routines for analyzing plate based flow cytometry data.
|
2023-06-16 |
|
kwip
|
public |
kWIP implements a de novo, alignment free measure of sample genetic dissimilarity
|
2023-06-16 |
