|
tigmint
|
public |
Correct misassemblies using linked or long reads
|
2025-03-25 |
|
bioconductor-elmer
|
public |
Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes
|
2025-03-25 |
|
bioconductor-elmer.data
|
public |
Data for the ELMER package
|
2025-03-25 |
|
r-seurat-scripts
|
public |
A set of wrappers for individual components of the Seurat package. Functions R packages are hard to call when building workflows outside of R, so this package adds a set of simple wrappers with robust argument parsing. Intermediate steps are currently mainly serialized R objects, but the ultimate objective is to have language-agnostic intermediate formats allowing composite workflows using a variety of software packages.
|
2025-03-25 |
|
r-workflowscriptscommon
|
public |
Common functions for making R function wapper scripts. Functions in R packages are hard to call when building workflows outside of R, so this package is used by other packages (e.g. r-seurat-scripts) to add sets of simple wrappers with robust argument parsing.
|
2025-03-25 |
|
scnic
|
public |
SCNIC: Sparse Cooccurence Network Investigation for Compositional data
|
2025-03-25 |
|
selene-sdk
|
public |
Framework for developing sequence-level deep learning networks.
|
2025-03-25 |
|
perl-mac-systemdirectory
|
public |
Locate Mac OS X Standard System Directories
|
2025-03-25 |
|
transgenescan
|
public |
Software tool for finding genes in assembled transcripts from metatranscriptomic sequences.
|
2025-03-25 |
|
perl-specio
|
public |
Type constraints and coercions for Perl
|
2025-03-25 |
|
perl-sub-quote
|
public |
Efficient generation of subroutines via string eval
|
2025-03-25 |
|
perl-module-list
|
public |
module `directory' listing
|
2025-03-25 |
|
perl-experimental
|
public |
Experimental features made easy
|
2025-03-25 |
|
perl-heap
|
public |
Perl extensions for keeping data partially sorted
|
2025-03-25 |
|
fithic
|
public |
Fit-Hi-C is a tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome architecture assays.
|
2025-03-25 |
|
teloclip
|
public |
A tool for the recovery of unassembled telomeres from soft-clipped read alignments.
|
2025-03-25 |
|
perl-sys-info
|
public |
Fetch information from the host system
|
2025-03-25 |
|
perl-sys-info-driver-osx
|
public |
OSX driver for Sys::Info
|
2025-03-25 |
|
perl-mac-propertylist
|
public |
work with Mac plists at a low level
|
2025-03-25 |
|
perl-xml-entities
|
public |
Mapping of XML entities to Unicode
|
2025-03-25 |
|
perl-math-random-mt-auto
|
public |
Auto-seeded Mersenne Twister PRNGs
|
2025-03-25 |
|
perl-parallel-loops
|
public |
Execute loops using parallel forked subprocesses
|
2025-03-25 |
|
perl-object-insideout
|
public |
Comprehensive inside-out object support module
|
2025-03-25 |
|
perl-math-complex
|
public |
trigonometric functions
|
2025-03-25 |
|
crux-toolkit
|
public |
A cross-platform suite of analysis tools for interpreting protein mass spectrometry data
|
2025-03-25 |
|
focus
|
public |
FOCUS is an innovative and agile model to profile and report organisms present in metagenomic samples based on composition usage without sequence length dependencies.
|
2025-03-25 |
|
perl-sys-info-driver-linux
|
public |
Linux driver for Sys::Info
|
2025-03-25 |
|
perl-devel-assert
|
public |
assertions for Perl >= 5.14
|
2025-03-25 |
|
perl-test-sys-info
|
public |
Centralized test suite for Sys::Info.
|
2025-03-25 |
|
perl-sys-info-base
|
public |
Base class for Sys::Info
|
2025-03-25 |
|
strike
|
public |
A program to evaluate protein multiple sequence alignments using a single protein structure.
|
2025-03-25 |
|
collect_mgf
|
public |
Collects MGF files and dd_results from an XMass setup_QDD.tcl experiment to a single MGF file.
|
2025-03-25 |
|
clairvoyante
|
public |
Identifying the variants of DNA sequences sensitively and accurately is an important but challenging task in the field of genomics. This task is particularly difficult when dealing with Single Molecule Sequencing, the error rate of which is still tens to hundreds of times higher than Next Generation Sequencing. With the increasing prevalence of Single Molecule Sequencing, an efficient variant caller will not only expedite basic research but also enable various downstream applications. To meet this demand, we developed Clairvoyante, a multi-task five-layer convolutional neural network model for predicting variant type, zygosity, alternative allele and Indel length. On NA12878, Clairvoyante achieved 99.73%, 97.68% and 95.36% accuracy on known variants, and achieved 98.65%, 92.57%, 77.89% F1 score on the whole genome, in Illumina, PacBio, and Oxford Nanopore data, respectively. Training Clairvoyante with a sample and call variant on another shows that Clairvoyante is sample agnostic and general for variant calling. A slim version of Clairvoyante with reduced model parameters produced a much lower F1, suggesting the full model's power in disentangling subtle details in read alignment. Clairvoyante is the first method for Single Molecule Sequencing to finish a whole genome variant calling in two hours on a 28 CPU-core machine, with top-tier accuracy and sensitivity. A toolset was developed to train, utilize and visualize the Clairvoyante model easily, and is publically available here is this repo.
|
2025-03-25 |
|
mapdia
|
public |
Performs essential data preprocessing, including novel retention time-based normalization method and a sequence of peptide/fragment selection steps, and more importantly, hierarchical model-based statistical significance analysis for multi-group comparisons under representative experimental designs.
|
2025-03-25 |
|
perl-business-isbn
|
public |
work with International Standard Book Numbers
|
2025-03-25 |
|
perl-business-isbn-data
|
public |
data pack for Business::ISBN
|
2025-03-25 |
|
somaticseq
|
public |
An ensemble approach to accurately detect somatic mutations.
|
2025-03-25 |
|
starfish
|
public |
Standardized analysis pipeline for image-based transcriptomics.
|
2025-03-25 |
|
slicedimage
|
public |
Python module to access sliced imaging data
|
2025-03-25 |
|
regional
|
public |
simple manipulation and display of spatial regions in python
|
2025-03-25 |
|
perl-string-truncate
|
public |
a module for when strings are too long to be displayed in...
|
2025-03-25 |
|
perl-string-rewriteprefix
|
public |
rewrite strings based on a set of known prefixes
|
2025-03-25 |
|
r-raceid
|
public |
Application of 'RaceID' allows inference of cell types and prediction of lineage trees by the StemID2 algorithm.
|
2025-03-25 |
|
perl-moosex-types-stringlike
|
public |
Moose type constraints for strings or string-like objects
|
2025-03-25 |
|
showit
|
public |
simple and sensible display of images in python
|
2025-03-25 |
|
r-fateid
|
public |
Application of 'FateID' allows computation and visualization of cell fate bias for multi-lineage single cell transcriptome data. Herman, J.S., Sagar, Grün D. (2017) <DOI:10.1038/nmeth.4662>.
|
2025-03-25 |
|
perl-carp-clan
|
public |
Report errors from perspective of caller of a "clan" of modules
|
2025-03-25 |
|
perl-sub-exporter-formethods
|
public |
helper routines for using Sub::Exporter to build methods
|
2025-03-25 |
|
perl-moosex-role-parameterized
|
public |
Moose roles with composition parameters
|
2025-03-25 |
|
perl-test-exec
|
public |
Test that some code calls exec without terminating testing
|
2025-03-25 |
