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pneumocat
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public |
PneumoCaT (Pneumococcal Capsular Typing) uses a two-step step approach to assign capsular type to S.pneumoniae genomic data (Illumina)
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2023-06-16 |
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r-metarnaseq
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public |
Implementation of two p-value combination techniques (inverse normal and Fisher methods). A vignette is provided to explain how to perform a meta-analysis from two independent RNA-seq experiments.
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2023-06-16 |
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picrust
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public |
PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States
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2023-06-16 |
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scanindel
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public |
ScanIndel is a python program to detect indels (insertions and deletions) from NGS data by re-align and de novo assemble soft clipped reads.
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2023-06-16 |
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cpinsim
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public |
CPINSim is a package for the simulation of protein complex assembly with constrained
protein interaction networks.
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2023-06-16 |
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rambo-k
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public |
a reference-based tool for rapid and sensitive extraction of one organism´s reads from a mixed NGS dataset
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2023-06-16 |
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perl-try-tiny-retry
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public |
Just like Try::Tiny, but with retry instead of try.
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2023-06-16 |
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perl-biox-workflow-command
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public |
Opinionated Bioinformatics Genomics Workflow Creator
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2023-06-16 |
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fgap
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public |
FGAP: an automated gap closing tool
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2023-06-16 |
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nanopore_simulation
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public |
Nanopore SimulatION is a tool for simulating an Oxfornd Nanopore Technologies MinION device for bioinformatic development.
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2023-06-16 |
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sis
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public |
A tool that uses mummer to scaffold small genomes.
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2023-06-16 |
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r-maldiquant
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public |
A complete analysis pipeline for matrix-assisted laser desorption/ionization-time-of-flight
(MALDI-TOF) and other two-dimensional mass spectrometry data. In addition to commonly
used plotting and processing methods it includes distinctive features, namely baseline
subtraction methods such as morphological filters (TopHat) or the statistics-sensitive
non-linear iterative peak-clipping algorithm (SNIP), peak alignment using warping
functions, handling of replicated measurements as well as allowing spectra with
different resolutions.
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2023-06-16 |
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haploclique
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public |
Viral quasispecies assembly via maximal clique finding. A method to reconstruct viral haplotypes and detect large insertions and deletions from NGS data.
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2023-06-16 |
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hg-color
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public |
HG-CoLoR (Hybrid Graph for the error Correction of Long Reads) is a hybrid method for the error correction of long reads that follows the main idea from NaS to produce corrected long reads from assemblies of related accurate short reads.
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2023-06-16 |
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progressivemauve
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public |
progressiveMauve computes multiple genome alignment with gene gain, loss and rearrangement
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2023-06-16 |
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plasmidtron
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public |
PlasmidTron: assembling the cause of phenotypes from NGS data
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2023-06-16 |
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deepmedic
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public |
Efficient Multi-Scale 3D Convolutional Neural Network for Brain Lesion Segmentation.
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2023-06-16 |
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linkage2allegro
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public |
Converts between the output linkage formats of Merlin, Simwalk, Genehunter, and Swiftlink into Allegro.
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2023-06-16 |
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sibelia
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public |
Genome comparison via de Bruijn graph.
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2023-06-16 |
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asn2gb
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public |
asn2gb converts ASN1 format sequence records to Genbank format
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2023-06-16 |
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ls-gkm
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public |
gkm-SVM, a sequence-based method for predicting regulatory DNA elements, is a useful tool for studying gene regulatory mechanisms. In continuous efforts to improve the method, new software, LS-GKM, is introduced. It offers much better scalability and provides further advanced gapped k-mer based kernel functions. As a result, LS-GKM achieves considerably higher accuracy than the original gkm-SVM.
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2023-06-16 |
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python-mailund-newick
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public |
Another python module to read and write the Newick format
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2023-06-16 |
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shortreadconnector
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public |
Short read connector enables the comparisons of two read sets
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2023-06-16 |
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python-newick
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public |
A python module to read and write the Newick format
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2023-06-16 |
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vcfkit
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public |
VCF-kit is a command-line based collection of utilities for performing analysis on Variant Call Format (VCF) files.
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2023-06-16 |
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pgsa
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public |
Pseudogenome Suffix Array is a compact index for collections of reads from sequencing.
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2023-06-16 |
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geodl
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public |
Download FASTQ files from GEO-NCBI and ENA with ease
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2023-06-16 |
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mzml2isa
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public |
mzml2isa - mzML to ISA-tab parsing tool
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2023-06-16 |
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parallel-fastq-dump
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public |
parallel fastq-dump wrapper
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2023-06-16 |
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ucsc-calc
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public |
Little command line calculator
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2023-06-16 |
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recycler
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public |
Recycler is a tool designed for extracting circular sequences from de novo assembly graphs
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2023-06-16 |
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graphclust-wrappers
|
public |
The set of individual perl wrappers extracted from GraphClust pipeline
|
2023-06-16 |
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pfam_scan
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public |
pfam_scan.pl is a Perl script calling HMMER v3 to search a FASTA file against a library of Pfam HMMs.
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2023-06-16 |
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r-snpassoc
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public |
This package carries out most common analysis when performing whole genome association studies. These analyses include descriptive statistics and exploratory analysis of missing values, calculation of Hardy-Weinberg equilibrium, analysis of association based on generalized linear models (either for quantitative or binary traits), and analysis of multiple SNPs (haplotype and epistasis analysis). Permutation test and related tests (sum statistic and truncated product) are also implemented. Max-statistic and genetic risk-allele score exact distributions are also possible to be estimated.
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2023-06-16 |
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metameta
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public |
MetaMeta - pipeline for integrating metagenome analysis tools to improve taxonomic profiling
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2023-06-16 |
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consensusfixer
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public |
Computes a consensus sequence with wobbles, ambiguous bases, and in-frame insertions, from a NGS read alignment.
|
2023-06-16 |
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r-pinfsc50
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public |
Genomic data for the plant pathogen "Phytophthora infestans." It includes a variant file ('VCF'), a sequence file ('FASTA') and an annotation file ('GFF'). This package is intended to be used as example data for packages that work with genomic data.
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2023-06-16 |
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bioconductor-rchemcpp
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public |
The Rchemcpp package implements the marginalized graph kernel and extensions, Tanimoto kernels, graph kernels, pharmacophore and 3D kernels suggested for measuring the similarity of molecules.
|
2023-06-16 |
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strainest
|
public |
Abundance estimation of strains
|
2023-06-16 |
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r-vcfr
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public |
Facilitates easy manipulation of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF files. Once VCF data is read into R a parser function extracts matrices of data. This information can then be used for quality control or other purposes. Additional functions provide visualization of genomic data. Once processing is complete data may be written to a VCF file (*.vcf.gz). It also may be converted into other popular R objects (e.g., genlight, DNAbin). VcfR provides a link between VCF data and familiar R software.
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2023-06-16 |
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sccaller
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public |
Dong X et al. Accurate identification of single-nucleotide variants in whole-genome-amplified single cells. Nat Methods. 2017 May;14(5):491-493. doi: 10.1038/nmeth.4227
|
2023-06-16 |
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bioconductor-imagehts
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public |
Analysis of high-throughput microscopy-based screens
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2023-06-16 |
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coprarna
|
public |
Target prediction for prokaryotic trans-acting small RNAs
|
2023-06-16 |
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r-haplo.stats
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public |
Routines for the analysis of indirectly measured haplotypes. The statistical methods assume that all subjects are unrelated and that haplotypes are ambiguous (due to unknown linkage phase of the genetic markers). The main functions are: haplo.em(), haplo.glm(), haplo.score(), and haplo.power(); all of which have detailed examples in the vignette.
|
2023-06-16 |
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r-ggsignif
|
public |
Enrich your 'ggplots' with group-wise comparisons. This package provides an easy way to indicate if two groups are significantly different. Commonly this is shown by a bracket on top connecting the groups of interest which itself is annotated with the level of significance (NS, *, **, ***). The package provides a single layer (geom_signif()) that takes the groups for comparison and the test (t.test(), wilcox.text() etc.) as arguments and adds the annotation to the plot.
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2023-06-16 |
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bioconductor-flipflop
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public |
Flipflop discovers which isoforms of a gene are expressed in a given sample together with their abundances, based on RNA-Seq read data. It takes an alignment file in SAM format as input. It can also discover transcripts from several samples simultaneously, increasing statistical power.
|
2023-06-16 |
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lohhla
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public |
A computational tool to evaluate HLA loss using next-generation sequencing data.
|
2023-06-16 |
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bioconductor-pgsea
|
public |
Parametric Gene Set Enrichment Analysis
|
2023-06-16 |
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bioconductor-flowrepositoryr
|
public |
FlowRepository R Interface
|
2023-06-16 |
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lcfit
|
public |
Likelihood curve fitting by nonlinear least squares.
|
2023-06-16 |
