|
r-fgwas
|
public |
GWAS tools for longitudinal genetic traits based on fGWAS statistical model.
|
2023-07-13 |
|
bioconductor-bgmix
|
public |
Bayesian models for differential gene expression
|
2023-07-12 |
|
r-samr
|
public |
Significance Analysis of Microarrays
|
2023-07-12 |
|
r-sleuth
|
public |
Tools for investigating RNA-Seq.
|
2023-07-12 |
|
bioconductor-multiomicsviz
|
public |
Plot the effect of one omics data on other omics data along the chromosome
|
2023-07-11 |
|
bioconductor-sscore
|
public |
S-Score Algorithm for Affymetrix Oligonucleotide Microarrays
|
2023-07-11 |
|
bioconductor-farms
|
public |
FARMS - Factor Analysis for Robust Microarray Summarization
|
2023-07-10 |
|
bioconductor-logitt
|
public |
logit-t Package
|
2023-07-10 |
|
bioconductor-clonality
|
public |
Clonality testing
|
2023-07-07 |
|
bioconductor-savr
|
public |
Parse and analyze Illumina SAV files
|
2023-07-07 |
|
bioconductor-flowmap
|
public |
Mapping cell populations in flow cytometry data for cross-sample comparisons using the Friedman-Rafsky Test
|
2023-07-07 |
|
bioconductor-pathvar
|
public |
Methods to Find Pathways with Significantly Different Variability
|
2023-07-07 |
|
perl-cpan-meta-requirements
|
public |
a set of version requirements for a CPAN dist
|
2023-07-07 |
|
svim
|
public |
SVIM is a structural variant caller for long reads.
|
2023-07-07 |
|
perl-http-date
|
public |
date conversion routines
|
2023-07-07 |
|
perl-statistics-descriptive
|
public |
Module of basic descriptive statistical functions.
|
2023-07-02 |
|
scprep
|
public |
Tools for loading and preprocessing biological matrices in Python.
|
2023-06-22 |
|
tassel
|
public |
TASSEL is a software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.
|
2023-06-22 |
|
clinvar-tsv
|
public |
A Snakemake-based program to download ClinVar and convert to easy-to-use TSV files.
|
2023-06-22 |
|
clairvoyante
|
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.
|
2023-06-16 |
|
bioconductor-sc3-scripts
|
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.
|
2023-06-16 |
|
abeona
|
public |
A simple transcriptome assembler based on kallisto and Cortex graphs.
|
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 |
|
scanpy
|
public |
Single-Cell Analysis in Python. Scales to >1M cells.
|
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 |
|
pypairs
|
public |
A python scRNA-Seq classifier
|
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 |
|
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 |
|
plantcv
|
public |
An image processing package for plant phenotyping.
|
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 |
|
kwip
|
public |
kWIP implements a de novo, alignment free measure of sample genetic dissimilarity
|
2023-06-16 |
|
consel
|
public |
CONSEL calculates the probability value (i.e., p-value) to assess the confidence in the selection problem. Although CONSEL is applicable to any selection problem, it is mainly designed for the phylogenetic tree selection
|
2023-06-16 |
|
r-taxonomizr
|
public |
Functions for assigning taxonomy to NCBI accession numbers and taxon IDs based on NCBI's accession2taxid and taxdump files. This package allows the user to downloads NCBI data dumps and create a local database for fast and local taxonomic assignment.
|
2023-06-16 |
|
bioconductor-prize
|
public |
Prize: an R package for prioritization estimation based on analytic hierarchy process
|
2023-06-16 |
|
bioconductor-clonotyper
|
public |
High throughput analysis of T cell antigen receptor sequences
|
2023-06-16 |
|
fast5-research
|
public |
ONT Research fast5 read/write package
|
2023-06-16 |
|
changeo
|
public |
A bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data. Citations: Gupta, et al (2015) <doi:10.1093/bioinformatics/btv359>.
|
2023-06-16 |
|
bioconductor-dupchecker
|
public |
a package for checking high-throughput genomic data redundancy in meta-analysis
|
2023-06-16 |
|
bioconductor-abadata
|
public |
Averaged gene expression in human brain regions from Allen Brain Atlas
|
2023-06-16 |
|
faststructure
|
public |
A variational framework for inferring population structure from SNP genotype data.
|
2023-06-16 |
|
calour
|
public |
exploratory and interactive microbiome analyses based on heatmaps
|
2023-06-16 |
|
perl-local-lib
|
public |
create and use a local lib/ for perl modules with PERL5LIB
|
2023-06-16 |
|
skmer
|
public |
Assembly-free and alignment-free tool for estimating genomic distances between genome-skims
|
2023-06-16 |
|
xpclr
|
public |
Code to compute xp-clr values to detect selection as per Chen, Patterson & Reich 2010.
|
2023-06-16 |
|
bioconductor-geneticsdesign
|
public |
Functions for designing genetics studies
|
2023-06-16 |
|
mirtrace
|
public |
miRTrace is a new quality control and taxonomic tracing tool developed specifically for small RNA sequencing data (sRNA-Seq).
Each sample is characterized by profiling sequencing quality, read length, sequencing depth and miRNA complexity and also the
amounts of miRNAs versus undesirable sequences (derived from tRNAs, rRNAs and sequencing artifacts). In addition to these routine
quality control (QC) analyses, miRTrace can accurately and sensitively resolve taxonomic origins of small RNA-Seq data based on the
composition of clade-specific miRNAs. This feature can be used to detect cross-clade contaminations in typical lab settings. It can
also be applied for more specific applications in forensics, food quality control and clinical diagnosis, for instance tracing the
origins of meat products or detecting parasitic microRNAs in host serum.
|
2023-06-16 |
