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Package Name Access Summary Updated
bioconductor-spectra public Spectra Infrastructure for Mass Spectrometry Data 2024-12-19
bioconductor-pvca public Principal Variance Component Analysis (PVCA) 2024-12-19
ntlink public Genome assembly scaffolder using long reads and minimizers 2024-12-19
bioconductor-spia public Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations 2024-12-19
r-nanostringnorm public A set of tools for normalizing, diagnostics and visualization of NanoString nCounter data. 2024-12-19
bioconductor-cola public A Framework for Consensus Partitioning 2024-12-19
bioconductor-doscheda public A DownStream Chemo-Proteomics Analysis Pipeline 2024-12-19
pygtftk public The gtftk suite providing facilities to manipulate genomic annotations in gtf format. 2024-12-19
bioconductor-interactivecomplexheatmap public Make Interactive Complex Heatmaps 2024-12-19
bioconductor-rvs public Computes estimates of the probability of related individuals sharing a rare variant 2024-12-19
bioconductor-lpnet public Linear Programming Model for Network Inference 2024-12-19
clair3-trio public Clair3-Trio is a variants caller tailored for family trios from nanopore long-reads. Clair3-Trio employs a Trio-to-Trio deep neural network model that allows it to input all trio’s sequencing information and output all trio’s predicted variants within a single model, to perform far better variant calling. We also present MCVLoss, the first loss function that can improve variants calling in trios by leveraging the explicitly encoding of the priors of the Mendelian inheritance in trios. Clair3-Trio showed comprehensive improvement in experiments. It predicted much fewer Mendelian inheritance violation variations than current state-of-the-art methods. 2024-12-19
bioconductor-affycontam public structured corruption of affymetrix cel file data 2024-12-19
ntsynt public Detecting multi-genome synteny blocks using minimizer graph mapping 2024-12-19
bioconductor-sparsearray public High-performance sparse data representation and manipulation in R 2024-12-19
bioconductor-flowdensity public Sequential Flow Cytometry Data Gating 2024-12-19
bioconductor-optimalflow public optimalFlow 2024-12-19
bioconductor-rcwlpipelines public Bioinformatics pipelines based on Rcwl 2024-12-19
tigmint public Correct misassemblies using linked or long reads 2024-12-19
bioconductor-trio public Testing of SNPs and SNP Interactions in Case-Parent Trio Studies 2024-12-19
bioconductor-simona public Semantic Similarity on Bio-Ontologies 2024-12-19
bioconductor-flowtrans public Parameter Optimization for Flow Cytometry Data Transformation 2024-12-19
ntjoin public Genome assembly scaffolder using minimizer graphs 2024-12-19
tiny-count public \ A precision counting tool for hierarchical classification and quantification of small RNA-seq reads. tiny-count is part of the tinyRNA analysis pipeline. 2024-12-19
clair3 public Clair3 is a small variant caller for long-reads. Compare to PEPPER (r0.4), Clair3 (v0.1) shows a better SNP F1-score with ≤30-fold of ONT data (precisionFDA Truth Challenge V2), and a better Indel F1-score, while runs generally four times faster. Clair3 makes the best of both worlds of using pileup or full-alignment as input for deep-learning based long-read small variant calling. Clair3 is simple and modular for easy deployment and integration. 2024-12-19
bioconductor-rexposome public Exposome exploration and outcome data analysis 2024-12-19
r-conos public Wires together large collections of single-cell RNA-seq datasets, which allows for both the identification of recurrent cell clusters and the propagation of information between datasets in multi-sample or atlas-scale collections. 'Conos' focuses on the uniform mapping of homologous cell types across heterogeneous sample collections. For instance, users could investigate a collection of dozens of peripheral blood samples from cancer patients combined with dozens of controls, which perhaps includes samples of a related tissue such as lymph nodes. This package interacts with data available through the 'conosPanel' package, which is available in a 'drat' repository. To access this data package, see the instructions at <https://github.com/kharchenkolab/conos>. The size of the 'conosPanel' package is approximately 12 MB. 2024-12-19
bioconductor-cardinalworkflows public Datasets and workflows for the Cardinal MSI 2024-12-19
bioconductor-ccplotr public Plots For Visualising Cell-Cell Interactions 2024-12-19
bioconductor-flowmerge public Cluster Merging for Flow Cytometry Data 2024-12-19
bioconductor-cnorfeeder public Integration of CellNOptR to add missing links 2024-12-19
bioconductor-ncigraph public Pathways from the NCI Pathways Database 2024-12-19
bioconductor-kcsmart public Multi sample aCGH analysis package using kernel convolution 2024-12-19
bioconductor-cghnormaliter public Normalization of array CGH data with imbalanced aberrations. 2024-12-19
multixrank public MultiXrank - heterogeneous MULTIlayer eXploration by RANdom walK with restart. MultiXrank is a Python package for the exploration of heterogeneous multilayer networks, with random walk with restart method. It permits prioritization of nodes between full heterogeneous networks, whatever their complexities. 2024-12-19
r-sew public SEW 2024-12-19
smaca public smaca is a python tool to detect putative SMA carriers and estimate the absolute SMN1 copy-number in a population. 2024-12-19
pysamstats public A Python utility for calculating statistics against genome position based on sequence alignments from a SAM, BAM or CRAM file. 2024-12-19
vcontact3 public Viral Contig Automatic Clustering and Taxonomy 2024-12-19
rmats2sashimiplot public rmats2sashimiplot 2024-12-19
velocyto.py public A library for the analysis of RNA velocity. 2024-12-19
htseq public HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments. 2024-12-19
bioconductor-spikeinsubset public Part of Affymetrix's Spike-In Experiment Data 2024-12-19
bioconductor-flowploidy public Analyze flow cytometer data to determine sample ploidy 2024-12-19
bioconductor-acgh public Classes and functions for Array Comparative Genomic Hybridization data 2024-12-19
bioconductor-tpp public Analyze thermal proteome profiling (TPP) experiments 2024-12-19
bioconductor-allmll public A subset of arrays from a large acute lymphoblastic leukemia (ALL) study 2024-12-19
bioconductor-mosbi public Molecular Signature identification using Biclustering 2024-12-19
bioconductor-rnits public R Normalization and Inference of Time Series data 2024-12-19
bioconductor-normqpcr public Functions for normalisation of RT-qPCR data 2024-12-19
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