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paramz
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public |
No Summary
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2025-03-25 |
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r-apcluster
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public |
No Summary
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2025-03-25 |
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pandoc
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public |
Universal markup converter (repackaged binaries)
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2025-03-25 |
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vim
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public |
No Summary
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2025-03-25 |
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r-annotables
|
public |
Provides tables for converting and annotating Ensembl Gene IDs
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2025-03-25 |
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r-rtsne
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public |
An R wrapper around the fast T-distributed Stochastic Neighbor Embedding implementation by Van der Maaten.
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2025-03-25 |
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r-logging
|
public |
logging is a pure R package that implements the ubiquitous log4j package.
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2025-03-25 |
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r-circlize
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public |
Circular layout is an efficient way for the visualization of huge amounts of information. Here the circlize package provides an implementation of circular layout generation in R as well as an enhancement of available software. The flexibility of this package is based on the usage of low-level graphics functions such that self-defined high-level graphics can be easily implemented by users for specific purposes. Together with the seamless connection between the powerful computational and visual environment in R, circlize gives users more convenience and freedom to design figures for better understanding complex patterns behind multi-dimensional data.
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2025-03-25 |
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scandir
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public |
scandir, a better directory iterator and faster os.walk()
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2025-03-25 |
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fastqp
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public |
Simple NGS read quality assessment using Python
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2025-03-25 |
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simplesam
|
public |
Simple pure Python SAM parser and objects for working with SAM records
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2025-03-25 |
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seaborn
|
public |
Seaborn: statistical data visualization
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2025-03-25 |
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bioconductor-ruvseq
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public |
This package implements the remove unwanted variation (RUV) methods of Risso et al. (2014) for the normalization of RNA-Seq read counts between samples.
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2025-03-25 |
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bioconductor-edaseq
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public |
Numerical and graphical summaries of RNA-Seq read data. Within-lane normalization procedures to adjust for GC-content effect (or other gene-level effects) on read counts: loess robust local regression, global-scaling, and full-quantile normalization (Risso et al., 2011). Between-lane normalization procedures to adjust for distributional differences between lanes (e.g., sequencing depth): global-scaling and full-quantile normalization (Bullard et al., 2010).
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2025-03-25 |
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bioconductor-aroma.light
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public |
Methods for microarray analysis that take basic data types such as matrices and lists of vectors. These methods can be used standalone, be utilized in other packages, or be wrapped up in higher-level classes.
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2025-03-25 |
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r-party
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public |
A computational toolbox for recursive partitioning. The core of the package is ctree(), an implementation of conditional inference trees which embed tree-structured regression models into a well defined theory of conditional inference procedures. This non-parametric class of regression trees is applicable to all kinds of regression problems, including nominal, ordinal, numeric, censored as well as multivariate response variables and arbitrary measurement scales of the covariates. Based on conditional inference trees, cforest() provides an implementation of Breiman's random forests. The function mob() implements an algorithm for recursive partitioning based on parametric models (e.g. linear models, GLMs or survival regression) employing parameter instability tests for split selection. Extensible functionality for visualizing tree-structured regression models is available.
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2025-03-25 |
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r-strucchange
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public |
Testing, monitoring and dating structural changes in (linear) regression models. strucchange features tests/methods from the generalized fluctuation test framework as well as from the F test (Chow test) framework. This includes methods to fit, plot and test fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F statistics, respectively. It is possible to monitor incoming data online using fluctuation processes. Finally, the breakpoints in regression models with structural changes can be estimated together with confidence intervals. Emphasis is always given to methods for visualizing the data.
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2025-03-25 |
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r-tree
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public |
Classification and regression trees.
|
2025-03-25 |
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bioconductor-tximport
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public |
Imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages. Average transcript length, weighted by sample-specific transcript abundance estimates, is provided as a matrix which can be used as an offset for different expression of gene-level counts.
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2025-03-25 |
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flask-table
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public |
HTML tables for use with the Flask micro-framework
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2025-03-25 |
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blinker
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None |
No Summary
|
2025-03-25 |
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flask-testing
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None |
No Summary
|
2025-03-25 |
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distance
|
public |
Utilities for comparing sequences
|
2025-03-25 |
|
bioconductor-all
|
public |
Data of T- and B-cell Acute Lymphocytic Leukemia from the Ritz Laboratory at the DFCI (includes Apr 2004 versions)
|
2025-03-25 |
|
lxml
|
None |
No Summary
|
2025-03-25 |
