Tools   Select Another Resource Report Type

https://bioconductor.org/packages/plyranges/

Open source software R package for interacting with common Bioconductor classes Ranges and GenomicRanges. Grammar of genomic data transformation. Provides grammatical and consistent way of manipulating these classes to increase accessiblity for new Bioconductor users.

Proper citation: plyranges (RRID:SCR_021324) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/ChIPseeker/

Software package to retrieve nearest genes around peak, annotate genomic region of peak, implements statstical methods for estimate significance of overlap among ChIP peak data sets, and incorporate GEO database for user to compare own dataset with those deposited in database.Several visualization functions are implemented to summarize coverage of peak experiment, average profile and heatmap of peaks binding to TSS regions, genomic annotation, distance to TSS, and overlap of peaks or genes.

Proper citation: ChIPseeker (RRID:SCR_021322) Copy   

•   Source: SciCrunch Registry

https://bioinf.shenwei.me/seqkit/

Software tool as cross platform and ultrafast toolkit for FASTA/Q file manipulation.

Proper citation: SeqKit (RRID:SCR_018926) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=mHG

Software R package to run minimum hypergeometric test.

Proper citation: Minimum-Hypergeometric Test (RRID:SCR_018776) Copy   

•   Source: SciCrunch Registry

https://gbrs.readthedocs.io/en/latest/

Software suite of tools for reconstructing genomes using RNA-Seq data from multiparent population and for quantifying allele specific expression.

Proper citation: GBRS (RRID:SCR_020963) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=survival

Software R package contains core survival analysis routines, including definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models.

Proper citation: survival (RRID:SCR_021137) Copy   

•   Source: SciCrunch Registry

https://github.com/smithlabcode/riborex

Software R package for identification of differential translation from Ribo-seq data. Computational tool for mapping genome wide differences in translation efficiency.

Proper citation: riborex (RRID:SCR_019104) Copy   

•   Source: SciCrunch Registry

https://pysam.readthedocs.io/en/latest/api.html

Software tool as interface for reading and writing SAM files. Python module to read and manipulate mapped short read sequence data stored in SAM/BAM files. Lightweight wrapper of htslib C-API.

Proper citation: pysam (RRID:SCR_021017) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=caret

Software R package provides misc functions for training and plotting classification and regression models.Contains tools for data splitting, pre-processing, feature selection, model tuning using resampling, and variable importance estimation, as well as other functionality.

Proper citation: caret (RRID:SCR_021138) Copy   

•   Source: SciCrunch Registry

https://github.com/anuprulez/galaxy_tool_recommendation

Software developed by analyzing workflows composed by researchers on European Galaxy server, using deep learning approach. Used to recommend tools in Galaxy. Gated recurrent units neural network.

Proper citation: Tool recommender system in Galaxy (RRID:SCR_018491) Copy   

•   Source: SciCrunch Registry

https://github.com/DReichLab/AdmixTools

Software package that supports formal tests of whether admixture occurred, and makes it possible to infer admixture proportions and dates.

Proper citation: ADMIXTOOLS (RRID:SCR_018495) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=openxlsx

Software R package to simplify creation of .xlsx files by providing high level interface to writing, styling and editing worksheets.

Proper citation: openxlsx (RRID:SCR_019185) Copy   

•   Source: SciCrunch Registry

https://github.com/ISA-tools/isa-api

Open platform for interoperable life science experimental metadata. Metadata framework as set of community specifications and software tools for enabling discovery, exchange and publication of metadata from experiments in life sciences. Python library for creation, editing, parsing, and validating of ISA-Tab and ISA-JSON formats.Provides programmatic metadata handling functionality to support automation, common interface and interoperable medium between two ISA formats, as well as with other life science data formats required for depositing data in public databases.

Proper citation: ISA API (RRID:SCR_020980) Copy   

•   Source: SciCrunch Registry

https://github.com/dorianps/LESYMAP

Software R package to conduct lesion-to-symptom mapping from human MRI data.Takes lesion maps and cognitive performance scores from patients with stroke, and maps brain areas responsible for cognitive deficit.

Proper citation: LESYMAP (RRID:SCR_017967) Copy   

•   Source: SciCrunch Registry

https://github.com/cosanlab/facesync

Open source software Python toolbox which automatically synchronizes recorded facial expressions to videos and events such as social interactions.Framework for recording facial expressions with head mounted cameras.

Proper citation: FaceSync (RRID:SCR_021396) Copy   

•   Source: SciCrunch Registry

https://github.com/UmSenhorQualquer/d-track/blob/master/docs/source/index.rst

Software package to track object in 3D based on 3D schematics of scene.Semi automatic 3D video tracking technique to analyse movements and routines of aquatic animals with application to captive dolphins.

Proper citation: D-Track (RRID:SCR_021394) Copy   

•   Source: SciCrunch Registry

https://www.7-zip.org

Open source software tool as file archiver with high compression ratio.

Proper citation: 7-Zip (RRID:SCR_021270) Copy   

•   Source: SciCrunch Registry

https://github.com/DeepLabCut/DeepLabCut

Open source software package for markerless pose estimation. 2D keypoint detection in animals.

Proper citation: DeepLabCut (RRID:SCR_021391) Copy   

•   Source: SciCrunch Registry

https://hoohm.github.io/CITE-seq-Count/

Software python package that allows to count antibody TAGS from CITE-seq and/or cell hashing experiment. Software tool that allows to get UMI counts from single cell protein assay. Used to count (UMI counts) antibody-derived-tags (ADTs) or Cell Hashing tags (HTOs) in raw sequencing reads and build count matrix.

Proper citation: CITE-seq-Count (RRID:SCR_019239) Copy   

•   Source: SciCrunch Registry

https://github.com/dorianps/LINDA

Software R package for automated segmentation of chronic stroke lesions. Automated segmentation algorithm capable of learning relationship between existing manual segmentations and single T1-weighted MRI.

Proper citation: LINDA (RRID:SCR_017971) Copy   

•   Source: SciCrunch Registry