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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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needletail
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public |
Fast FASTX parsing in Python
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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
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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
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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.
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2024-12-19 |
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bioconductor-spikeinsubset
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public |
Part of Affymetrix's Spike-In Experiment Data
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2024-12-19 |
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bioconductor-flowploidy
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public |
Analyze flow cytometer data to determine sample ploidy
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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
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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
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2024-12-19 |
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bioconductor-mosbi
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public |
Molecular Signature identification using Biclustering
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2024-12-19 |
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bioconductor-rnits
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public |
R Normalization and Inference of Time Series data
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2024-12-19 |
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bioconductor-normqpcr
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public |
Functions for normalisation of RT-qPCR data
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2024-12-19 |
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motifscan
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public |
A package for motif discovery and motif enrichment analysis
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2024-12-19 |
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bioconductor-plier
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public |
Implements the Affymetrix PLIER algorithm
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2024-12-19 |
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umi_tools
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public |
Tools for dealing with Unique Molecular Identifiers (UMIs) / Random Molecular Tags (RMTs).
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2024-12-19 |
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bioconductor-flowviz
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public |
Visualization for flow cytometry
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2024-12-19 |
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bioconductor-anota
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public |
ANalysis Of Translational Activity (ANOTA).
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2024-12-19 |
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devider
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public |
Haplotyping small sequences from heterogeneous long-read sequencing samples with a SNP-encoded positional de Bruijn graphs.
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2024-12-19 |
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r-grain
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public |
Probability propagation in graphical independence networks, also known as Bayesian networks or probabilistic expert systems.
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2024-12-19 |
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r-genomictools
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public |
A loose collection of tools for the analysis of expression and genotype data, currently with the main focus on (e)QTL and MDR analysis.
|
2024-12-19 |
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r-pcalg
|
public |
Functions for causal structure learning and causal inference using graphical models. The main algorithms for causal structure learning are PC (for observational data without hidden variables), FCI and RFCI (for observational data with hidden variables), and GIES (for a mix of data from observational studies (i.e. observational data) and data from experiments involving interventions (i.e. interventional data) without hidden variables). For causal inference the IDA algorithm, the Generalized Backdoor Criterion (GBC), the Generalized Adjustment Criterion (GAC) and some related functions are implemented. Functions for incorporating background knowledge are provided.
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2024-12-19 |
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bioconductor-frmatools
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public |
Frozen RMA Tools
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2024-12-19 |
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bioconductor-liebermanaidenhic2009
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public |
Selected data from the HiC paper of E. Lieberman-Aiden et al. in Science (2009)
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2024-12-19 |
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bioconductor-eximir
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public |
R functions for the normalization of Exiqon miRNA array data
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2024-12-19 |
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bioconductor-s4arrays
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public |
Foundation of array-like containers in Bioconductor
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2024-12-19 |
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r-isogene
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public |
Offers framework for testing for monotonic relationship between gene expression and doses in a microarray experiment. Several testing procedures including the global likelihood-ratio test (Bartholomew, 1961), Williams (1971, 1972), Marcus (1976), M (Hu et al. 2005) and the modified M (Lin et al. 2007) are used to test for the monotonic trend in gene expression with respect to doses. BH (Benjamini and Hochberg 1995) and BY (Benjamini and Yekutieli 2004) FDR controlling procedures are applied to adjust the raw p-values obtained from the permutations.
|
2024-12-19 |
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bioconductor-hapfabia
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public |
hapFabia: Identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data
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2024-12-19 |
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abyss
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public |
Assembly By Short Sequences - a de novo, parallel, paired-end short read sequence assembler.
|
2024-12-19 |
