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bioconductor-deqms
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public |
a tool to perform statistical analysis of differential protein expression for quantitative proteomics data.
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2025-04-22 |
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gvcfgenotyper
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public |
A utility for merging and genotyping Illumina-style GVCFs.
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2025-04-22 |
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r-nam
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public |
Designed for association studies in nested association mapping (NAM) panels, experimental and random panels. The method is described by Xavier et al. (2015) <doi:10.1093/bioinformatics/btv448>. It includes tools for genome-wide associations of multiple populations, marker quality control, population genetics analysis, genome-wide prediction, solving mixed models and finding variance components through likelihood and Bayesian methods.
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2025-04-22 |
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r-corbi
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public |
Provides a bundle of basic and fundamental bioinformatics tools, such as network querying and alignment, subnetwork extraction and search, network biomarker identification.
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2025-04-22 |
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changeo
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public |
A bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data.
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2025-04-22 |
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r-loom
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public |
An interface for the single-cell RNAseq-oriented loom format. Loom files are an HDF5-based format for storing and interacting with large single-cell RNAseq datasets. loomR provides an interface for working with loom files in a loom-specific way; we provide routines for validating loom files, iterating with chunks through data within the loom file, and provide a platform for other packages to build support for loom files.
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2025-04-22 |
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nimnexus
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public |
command-line tools for processing ChIP-nexus data
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2025-04-22 |
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airr
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public |
AIRR Community Data Representation Standard reference library for antibody and TCR sequencing data. Citations: AIRR standards <doi:10.5281/zenodo.1185414>.
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2025-04-22 |
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r-tigger
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public |
Infers the V genotype of an individual from immunoglobulin (Ig) repertoire sequencing data (AIRR-Seq, Rep-Seq). Includes detection of any novel alleles. This information is then used to correct existing V allele calls from among the sample sequences. Citations: Gadala-Maria, et al (2015) <doi:10.1073/pnas.1417683112>.
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2025-04-22 |
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r-mvr
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public |
This is a non-parametric method for joint adaptive mean-variance regularization and variance stabilization of high-dimensional data. It is suited for handling difficult problems posed by high-dimensional multivariate datasets (p >> n paradigm). Among those are that the variance is often a function of the mean, variable-specific estimators of variances are not reliable, and tests statistics have low powers due to a lack of degrees of freedom. Key features include: (i) Normalization and/or variance stabilization of the data, (ii) Computation of mean-variance-regularized t-statistics (F-statistics to follow), (iii) Generation of diverse diagnostic plots, (iv) Computationally efficient implementation using C/C++ interfacing and an option for parallel computing to enjoy a faster and easier experience in the R environment.
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2025-04-22 |
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perl-findbin-real
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public |
Locates the full path to the script bin directory to allow the use of paths relative to the bin directory.
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2025-04-22 |
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r-airr
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public |
Schema definitions and read, write and validation tools for data formatted in accordance with the AIRR Data Representation schemas defined by the AIRR Community <http://docs.airr-community.org>.
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2025-04-22 |
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ncrf
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public |
Noise-Cancelling Repeat Finder, Uncovering tandem repeats in error-prone long-read sequencing data.
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2025-04-22 |
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blockclust
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public |
Efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles.
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2025-04-22 |
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deeptoolsintervals
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public |
A python module creating/accessing GTF-based interval trees with associated meta-data
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2025-04-22 |
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perl-clone-choose
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public |
Choose appropriate clone utility
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2025-04-22 |
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r-lncpipereporter
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public |
Automatically Aggregating and Summarizing lncRNA Analysis Results for Interactive Report
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2025-04-22 |
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r-classdiscovery
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public |
Defines the classes used for "class discovery" problems in the OOMPA project (<http://oompa.r-forge.r-project.org/>). Class discovery primarily consists of unsupervised clustering methods with attempts to assess their statistical significance.
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2025-04-22 |
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cocoscore
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public |
CoCoScore: context-aware co-occurrence scores for biomedical text mining applications
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2025-04-22 |
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diamond_add_taxonomy
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public |
Utility to work with NCBI taxonomy database including tool to annotate DIAMOND results with taxonomy lineage
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2025-04-22 |
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wgfast
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public |
The whole genome focused array SNP typing (WG-FAST) pipeline
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2025-04-22 |
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qcat
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public |
Qcat is Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files.
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2025-04-22 |
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demuxlet
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public |
Genetic multiplexing of barcoded single cell RNA-seq
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2025-04-22 |
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parasail-python
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public |
Python bindings for the parasail C library containing implementations of pairwise sequence alignment algorithms.
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2025-04-22 |
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rgt
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public |
Toolkit to perform regulatory genomics data analysis
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2025-04-22 |
