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bioconductor-pvca
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public |
Principal Variance Component Analysis (PVCA)
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2024-12-19 |
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ntlink
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public |
Genome assembly scaffolder using long reads and minimizers
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2024-12-19 |
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bioconductor-spia
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public |
Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations
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2024-12-19 |
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r-nanostringnorm
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public |
A set of tools for normalizing, diagnostics and visualization of NanoString nCounter data.
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2024-12-19 |
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bioconductor-cola
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public |
A Framework for Consensus Partitioning
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2024-12-19 |
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bioconductor-doscheda
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public |
A DownStream Chemo-Proteomics Analysis Pipeline
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2024-12-19 |
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pygtftk
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public |
The gtftk suite providing facilities to manipulate genomic annotations in gtf format.
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2024-12-19 |
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bioconductor-interactivecomplexheatmap
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public |
Make Interactive Complex Heatmaps
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2024-12-19 |
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bioconductor-rvs
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public |
Computes estimates of the probability of related individuals sharing a rare variant
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2024-12-19 |
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bioconductor-lpnet
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public |
Linear Programming Model for Network Inference
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2024-12-19 |
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clair3-trio
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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.
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2024-12-19 |
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bioconductor-affycontam
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public |
structured corruption of affymetrix cel file data
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2024-12-19 |
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ntsynt
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public |
Detecting multi-genome synteny blocks using minimizer graph mapping
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2024-12-19 |
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bioconductor-sparsearray
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public |
High-performance sparse data representation and manipulation in R
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2024-12-19 |
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bioconductor-flowdensity
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public |
Sequential Flow Cytometry Data Gating
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2024-12-19 |
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bioconductor-optimalflow
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public |
optimalFlow
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2024-12-19 |
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bioconductor-rcwlpipelines
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public |
Bioinformatics pipelines based on Rcwl
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2024-12-19 |
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tigmint
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public |
Correct misassemblies using linked or long reads
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2024-12-19 |
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bioconductor-trio
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public |
Testing of SNPs and SNP Interactions in Case-Parent Trio Studies
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2024-12-19 |
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bioconductor-simona
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public |
Semantic Similarity on Bio-Ontologies
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2024-12-19 |
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bioconductor-flowtrans
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public |
Parameter Optimization for Flow Cytometry Data Transformation
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2024-12-19 |
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ntjoin
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public |
Genome assembly scaffolder using minimizer graphs
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2024-12-19 |
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tiny-count
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public |
\ A precision counting tool for hierarchical classification and quantification of small RNA-seq reads. tiny-count is part of the tinyRNA analysis pipeline.
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2024-12-19 |
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clair3
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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.
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2024-12-19 |
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bioconductor-rexposome
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public |
Exposome exploration and outcome data analysis
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2024-12-19 |
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hatchet
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public |
A package to infer allele and clone-specific copy-number aberrations (CNAs).
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2024-12-19 |
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r-conos
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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.
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2024-12-19 |
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bioconductor-cardinalworkflows
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public |
Datasets and workflows for the Cardinal MSI
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2024-12-19 |
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bioconductor-ccplotr
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public |
Plots For Visualising Cell-Cell Interactions
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2024-12-19 |
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bioconductor-flowmerge
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public |
Cluster Merging for Flow Cytometry Data
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2024-12-19 |
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bioconductor-cnorfeeder
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public |
Integration of CellNOptR to add missing links
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2024-12-19 |
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bioconductor-ncigraph
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public |
Pathways from the NCI Pathways Database
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2024-12-19 |
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bioconductor-kcsmart
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public |
Multi sample aCGH analysis package using kernel convolution
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2024-12-19 |
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bioconductor-cghnormaliter
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public |
Normalization of array CGH data with imbalanced aberrations.
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2024-12-19 |
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multixrank
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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.
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2024-12-19 |
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r-sew
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public |
SEW
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2024-12-19 |
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smaca
|
public |
smaca is a python tool to detect putative SMA carriers and estimate the absolute SMN1 copy-number in a population.
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2024-12-19 |
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pysamstats
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public |
A Python utility for calculating statistics against genome position based on sequence alignments from a SAM, BAM or CRAM file.
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2024-12-19 |
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vcontact3
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public |
Viral Contig Automatic Clustering and Taxonomy
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2024-12-19 |
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rmats2sashimiplot
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public |
rmats2sashimiplot
|
2024-12-19 |
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velocyto.py
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public |
A library for the analysis of RNA velocity.
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2024-12-19 |
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htseq
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public |
HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
|
2024-12-19 |
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bioconductor-spikeinsubset
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public |
Part of Affymetrix's Spike-In Experiment Data
|
2024-12-19 |
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bioconductor-flowploidy
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public |
Analyze flow cytometer data to determine sample ploidy
|
2024-12-19 |
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bioconductor-acgh
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public |
Classes and functions for Array Comparative Genomic Hybridization data
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2024-12-19 |
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bioconductor-tpp
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public |
Analyze thermal proteome profiling (TPP) experiments
|
2024-12-19 |
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bioconductor-allmll
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public |
A subset of arrays from a large acute lymphoblastic leukemia (ALL) study
|
2024-12-19 |
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bioconductor-mosbi
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public |
Molecular Signature identification using Biclustering
|
2024-12-19 |
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bioconductor-rnits
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public |
R Normalization and Inference of Time Series data
|
2024-12-19 |
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bioconductor-normqpcr
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public |
Functions for normalisation of RT-qPCR data
|
2024-12-19 |
