|
r-extrafontdb
|
public |
Package for holding the database for the extrafont package
|
2025-04-22 |
|
r-rttf2pt1
|
public |
Contains the program 'ttf2pt1', for use with the 'extrafont' package. This product includes software developed by the 'TTF2PT1' Project and its contributors.
|
2025-04-22 |
|
behst
|
public |
BEHST reads an input dataset of chromosome regions, and intersects them with the chromatin interactions available in the Hi-C dataset. Of these chromosome regions, BEHST selects those that are presentthe regulatory regions of genes of APPRIS, a dataset of principal isoform annotations. We defined these cis-regulatory regions upon the position of their nearest transcription start site of the APPRIS genes' principal transcripts (obtained through GENCODE), plus an upstream and downstream extension. Afterwards, BEHST takes the genes of the resulting partner loci found in gene regulatory regions, and performs a gene set enrichment analysis on them through g:Profiler. BEHST, finally, outputs the list of the most significant Gene Ontology terms detected by g:Profiler. Citation: Davide Chicco, Haixin Sarah Bi, Juri Reimand, and Michael M. Hoffman, 'BEHST: Genomic set enrichment analysis enhanced through integration of chromatin long-range interactions', 2018. In preparation. Website: http://behst.hoffmanlab.org/
|
2025-04-22 |
|
vdjer
|
public |
B Cell Receptor Repertoire Reconstruction from short read mRNA-Seq data
|
2025-04-22 |
|
imseq
|
public |
IMSEQ is a fast, PCR and sequencing error aware tool to analyze high throughput data from recombined T-cell receptor or immunoglobulin gene sequencing experiments
|
2025-04-22 |
|
nanosv
|
public |
Structural variation detection tool for Oxford Nanopore data.
|
2025-04-22 |
|
helperlibs
|
public |
A collection of bioinformatics-related helper functions
|
2025-04-22 |
|
pyquery
|
public |
A jquery-like library for python
|
2025-04-22 |
|
adam
|
public |
Genomics analysis platform built on Apache Avro, Apache Spark, and Apache Parquet
|
2025-04-22 |
|
ecopy
|
public |
EcoPy: Ecological Data Analysis in Python
|
2025-04-22 |
|
rust-overlaps
|
public |
A fast and secure command line utilility for enumerating all suffix-prefix
overlaps within a set of sequences, satisfying a user-specified minimal
overlap length and maximal error rate.
|
2025-04-22 |
|
minimock
|
public |
The simplest possible mock library
|
2025-04-22 |
|
r-flexclust
|
public |
The main function kcca implements a general framework for k-centroids cluster analysis supporting arbitrary distance measures and centroid computation. Further cluster methods include hard competitive learning, neural gas, and QT clustering. There are numerous visualization methods for cluster results (neighborhood graphs, convex cluster hulls, barcharts of centroids, ...), and bootstrap methods for the analysis of cluster stability.
|
2025-04-22 |
|
r-fpc
|
public |
Various methods for clustering and cluster validation. Fixed point clustering. Linear regression clustering. Clustering by merging Gaussian mixture components. Symmetric and asymmetric discriminant projections for visualisation of the separation of groupings. Cluster validation statistics for distance based clustering including corrected Rand index. Cluster-wise cluster stability assessment. Methods for estimation of the number of clusters: Calinski-Harabasz, Tibshirani and Walther's prediction strength, Fang and Wang's bootstrap stability. Gaussian/multinomial mixture fitting for mixed continuous/categorical variables. Variable-wise statistics for cluster interpretation. DBSCAN clustering. Interface functions for many clustering methods implemented in R, including estimating the number of clusters with kmeans, pam and clara. Modality diagnosis for Gaussian mixtures.
|
2025-04-22 |
|
r-reshape
|
public |
Flexibly restructure and aggregate data using just melt() and cast().
|
2025-04-22 |
|
r-kernlab
|
public |
Kernel-based machine learning methods for classification, regression, clustering, novelty detection, quantile regression and dimensionality reduction. Among other methods 'kernlab' includes Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes and a QP solver.
|
2025-04-22 |
|
r-diptest
|
public |
Compute Hartigan's dip test statistic for unimodality / multimodality and provide a test with simulation based p-values, where the original public code has been corrected.
|
2025-04-22 |
|
r-e1071
|
public |
Functions for latent class analysis, short time Fourier transform, fuzzy clustering, support vector machines, shortest path computation, bagged clustering, naive Bayes classifier, ...
|
2025-04-22 |
|
r-trimcluster
|
public |
Trimmed k-means clustering.
|
2025-04-22 |
|
r-prabclus
|
public |
Distance-based parametric bootstrap tests for clustering with spatial neighborhood information. Some distance measures, Clustering of presence-absence, abundance and multilocus genetical data for species delimitation, nearest neighbor based noise detection. Try package?prabclus for on overview.
|
2025-04-22 |
|
r-flexmix
|
public |
A general framework for finite mixtures of regression models using the EM algorithm is implemented. The package provides the E-step and all data handling, while the M-step can be supplied by the user to easily define new models. Existing drivers implement mixtures of standard linear models, generalized linear models and model-based clustering.
|
2025-04-22 |
|
tabix
|
public |
C library and command line tools for high-throughput sequencing data formats.
|
2025-04-22 |
|
basic
|
public |
BASIC is a semi-de novo assembly method for assembling BCR and TCR genes from single cell RNA-seq data.
|
2025-04-22 |
|
pysvg
|
public |
Python SVG Library
|
2025-04-22 |
|
pyexcelerator
|
public |
generating Excel 97+ files; importing Excel 95+ files; Excel files dumper; OLE2 files dumper; xls2txt, xls2csv, xls2html
|
2025-04-22 |
