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carnac-lr
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public |
Clustering coefficient-based Acquisition of RNA Communities in Long Read
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2024-12-12 |
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repaq
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public |
A fast lossless FASTQ compressor with ultra-high compression ratio
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2024-12-12 |
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blockbuster
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public |
Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach.
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2024-12-12 |
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r-seurat-disk
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public |
The h5Seurat file format is specifically designed for the storage and analysis of multi-modal single-cell and spatially-resolved expression experiments, for example, from CITE-seq or 10X Visium technologies. It holds all molecular information and associated metadata, including (for example) nearest-neighbor graphs, dimensional reduction information, spatial coordinates and image data, and cluster labels. We also support rapid and on-disk conversion between h5Seurat and AnnData objects, with the goal of enhancing interoperability between Seurat and Scanpy.
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2024-12-12 |
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gtfsort
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public |
A chr/pos/feature GTF sorter that uses a lexicographically-based index ordering algorithm.
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2024-12-12 |
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ucsc-transmappsltogenepred
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public |
convert PSL alignments of mRNAs to gene annotations.
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2024-12-12 |
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porechop_abi
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public |
Adapter inferrence and removal of Oxford Nanopore reads
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2024-12-12 |
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wtdbg
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public |
Wtdbg2: A fuzzy Bruijn graph approach to long noisy reads assembly
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2024-12-12 |
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pbjasmine
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public |
jasmine
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2024-12-12 |
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survivor
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public |
Toolset for SV simulation, comparison and filtering
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2024-12-12 |
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genion
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public |
Characterizing gene fusions using long transcriptomics reads
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2024-12-12 |
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netcdf-metadata-info
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public |
Metadata information from netcdf file for Galaxy use.
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2024-12-12 |
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haplink
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public |
Viral haplotype calling via linkage disequilibrium
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2024-12-12 |
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fingerprintscan
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public |
Search against FingerPRINTScan with a protein query sequence to identify the closest matching PRINTS sequence motif fingerprints in a protein sequence.
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2024-12-12 |
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sabre
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public |
A barcode demultiplexing and trimming tool for FastQ files
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2024-12-12 |
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bwa
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public |
The BWA read mapper.
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2024-12-12 |
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fermi
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public |
A WGS de novo assembler based on the FMD-index for large genomes
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2024-12-12 |
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cmph
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public |
No Summary
|
2024-12-12 |
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merfishtools
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public |
MERFISHtools implement a Bayesian framework for accurately predicting gene or transcript expression from MERFISH data. On top, differential expression analysis can be performed for two or multiple conditions, including credible intervals for fold change and coefficient of variation, and controlling the expected false discovery rate.
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2024-12-12 |
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bgt
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public |
Flexible genotype query among 30,000+ samples whole-genome.
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2024-12-12 |
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classpro
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public |
A K-mer classifier for HiFi reads .
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2024-12-12 |
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pysais
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public |
Suffix array computation with induced sorting algorithm.
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2024-12-12 |
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pb-falconc
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public |
C utilities for PacBio assembly (pbipa etc.)
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2024-12-12 |
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ucsc-bigmaftomaf
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public |
convert bigMaf to maf file
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2024-12-12 |
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ucsc-bigbednameditems
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public |
Extract item of given name from bigBed
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2024-12-12 |
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conus
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public |
CONUS is an implementation of simple stochastic context-free grammars for RNA secondary structure analysis.CONUS developed for exploring the consequences of different single sequence SCFG designs in predicting RNA secondary structure.
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2024-12-12 |
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spoa
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public |
SIMD partial order alignment tool/library
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2024-12-12 |
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dazz_db
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public |
DAZZ_DB: The Dazzler Data Base
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2024-12-12 |
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biobloomtools
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public |
Building Bloom filters and using them for categorizing sequences
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2024-12-12 |
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coverageanomalyscanner
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public |
Application to find local anomalies in read coverage and to predict putative SV events.
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2024-12-12 |
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smashpp
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public |
A fast tool to find and visualize rearrangements in DNA sequences
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2024-12-12 |
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ucsc-bigwiginfo
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public |
Print out information about bigWig file.
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2024-12-12 |
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get_fasta_info
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public |
get_FAST{A,Q}_info - Get fast info on fasta and fastq files
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2024-12-12 |
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simwalk2
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public |
Stochastic Statistical Analysis of Qualitative Traits
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2024-12-12 |
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fastq-multx
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public |
Demultiplexes a fastq. Capable of auto-determining barcode id's based on a master set fields. Keeps multiple reads in-sync during demultiplexing. Can verify that the reads are in-sync as well, and fail if they're not.
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2024-12-12 |
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ucsc-bedsort
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public |
Sort a .bed file by chrom,chromStart
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2024-12-12 |
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r-buencolors
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public |
R utility package for color mapping and plot aesthetics.
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2024-12-12 |
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ucsc-rowstocols
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public |
Convert rows to columns and vice versa in a text file.
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2024-12-12 |
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r-sbpiper
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public |
Provides an API for analysing repetitive parameter estimations and simulations of mathematical models. Examples of mathematical models are Ordinary Differential equations (ODEs) or Stochastic Differential Equations (SDEs) models. Among the analyses for parameter estimation 'sbpiper' calculates statistics and generates plots for parameter density, PCA of the best fits, parameter profile likelihood estimations (PLEs), and 2D parameter PLEs. These results can be generated using all or a subset of the best computed parameter sets. Among the analyses for model simulation 'sbpiper' calculates statistics and generates plots for deterministic and stochastic time courses via cartesian and heatmap plots. Plots for the scan of one or two model parameters can also be generated. This package is primarily used by the software 'SBpipe'. Citation: Dalle Pezze P, Le Novère N. SBpipe: a collection of pipelines for automating repetitive simulation and analysis tasks. BMC Systems Biology. 2017;11:46. <doi:10.1186/s12918-017-0423-3>.
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2024-12-12 |
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cyntenator
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public |
progressive gene order alignments
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2024-12-12 |
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cmaple
|
public |
MAximum Parsimonious Likelihood Estimation in C/C++.
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2024-12-12 |
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cesar
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public |
CESAR 2.0 is a method to realign coding exons or genes to DNA sequences using a Hidden Markov Model
|
2024-12-12 |
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ucsc-overlapselect
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public |
Select records based on overlapping chromosome ranges. The ranges are specified in the selectFile, with each block specifying a range. Records are copied from the inFile to outFile based on the selection criteria. Selection is based on blocks or exons rather than entire range.
|
2024-12-12 |
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ucsc-spacedtotab
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public |
Convert fixed width space separated fields to tab separated
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2024-12-12 |
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ema
|
public |
Fast & accurate alignment of barcoded short-reads
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2024-12-12 |
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dwgsim
|
public |
Whole Genome Simulator for Next-Generation Sequencing
|
2024-12-12 |
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fastq-count
|
public |
Simple fastq read and base counter for paired data.
|
2024-12-12 |
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msaprobs
|
public |
MSAProbs is a well-established state-of-the-art multiple sequence alignment algorithm for protein sequences.
|
2024-12-12 |
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r-mcpcounter
|
public |
Estimating tissue-infiltrating immune and other stromal subpopulations abundances using gene expression
|
2024-12-12 |
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fastq-pair
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public |
fastq-pair: efficient synchronization of paired-end fastq files
|
2024-12-12 |
