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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
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
https://github.com/vinguyenle/k-FLBPCM-method
Software tool as novel k-FLBPCM method for detecting morphologically similar crops and weeds based on combination of contour masks and Local Binary Pattern operators.
Proper citation: k-FLBPCM method (RRID:SCR_017973) Copy
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
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
https://www.flidea.tech/flic-support
Software tool as user interface for running Fly Liquid Food Interaction Counter experiments.
Proper citation: FLIC Monitor (RRID:SCR_018387) Copy
https://w3.psychology.su.se/sleipner/
Software package as collection of modules implementing methods of analysis that form self-contained and empirically grounded toolbox for handling longitudinal data within person oriented paradigm.
Proper citation: sleipner (RRID:SCR_018143) Copy
https://pypi.org/project/pyani/
Software package and script for calculation of genome scale average nucleotide identity. Python3 module that provides support for calculating average nucleotide identity and related measures for whole genome comparisons, and rendering relevant graphical summary output. Where available, it takes advantage of multicore systems, and can integrate with SGE/OGE-type job schedulers for the sequence comparisons.
Proper citation: Pyani (RRID:SCR_021088) Copy
https://bioconductor.org/packages/FilterFFPE/
Software R package to find and filter artificial chimeric reads specifically generated in next generation sequencing process of formalin fixed paraffin embedded tissues. These artificial chimeric reads can lead to large number of false positive structural variant calls. Artifact chimeric read filter to improve SV detection in FFPE samples.
Proper citation: FilterFFPE (RRID:SCR_021086) Copy
http://bioconductor.org/packages/org.Rn.eg.db/
Software R tool for genome wide annotation for Rat, primarily based on mapping using Entrez Gene identifiers.
Proper citation: org.Rn.eg.db (RRID:SCR_018358) Copy
https://github.com/sdorkenw/MeshParty
Software package for working with neuronal meshes, skeletons, and annotations from electron microscopy data. Used to work with meshes, designed around use cases for analyzing neuronal morphology.
Proper citation: MeshParty (RRID:SCR_021873) Copy
https://github.com/bondarevts/flucalc
Software tool as MSS-MLE calculator for Luria–Delbrück fluctuation analysis.
Proper citation: FluCalc (RRID:SCR_019322) Copy
https://github.com/wehr-lab/autopilot
Software tool as open source Python framework for behavioral neuroscience that distributes experiments over networked swarms of Raspberry Pis. Toolkit of flexible modules to design experiments without rigid programming and API limitations.
Proper citation: AutoPilot (RRID:SCR_021518) Copy
https://github.com/ParBLiSS/FastANI
Software tool for fast alignment free computation of whole genome Average Nucleotide Identity . Supports pairwise comparison of both complete and draft genome assemblies. to calcualte the average nucleotide identity (ANI) between your samples.
Proper citation: FastANI (RRID:SCR_021091) Copy
https://iopscience.iop.org/article/10.1088/0957-0233/20/10/104035
Software package for advanced time domain analysis of magnetic resonance spectroscopy (MRS) and spectroscopic imaging (MRSI) data.
Proper citation: jMRUI (RRID:SCR_021893) Copy
https://github.com/oushujun/EDTA
Software package to filter out false discoveries in raw TE candidates and generate high quality non redundant TE library for whole genome TE annotations.Produces filtered non redundant TE library for annotation of structurally intact and fragmented elements.
Proper citation: EDTA (RRID:SCR_022063) Copy
https://github.com/jgraving/DeepPoseKit
Software toolkit with high level API for 2D pose estimation of user defined keypoints using deep learning.Written in Python and built using Tensorflow and Keras.Method for pose estimation developed by behavioral scientists at the Max Planck Institute of Animal Behavior.
Proper citation: DeepPoseKit (RRID:SCR_021405) Copy
https://neurokit2.readthedocs.io/en/latest/
Software Python package for neurophysiological signal processing. Used to analyze physiological data.
Proper citation: Neurokit2 (RRID:SCR_021889) Copy
https://bioconductor.org/packages/EpiDISH/
Software R package provides tools to infer proportions of priori known cell-types present in sample representing mixture of such cell-types. Comparison of reference based algorithms for correcting cell-type heterogeneity in Epigenome-Wide Association Studies.
Proper citation: EpiDISH R package (RRID:SCR_018004) Copy
https://github.com/DrCoffey/DeepSqueak
Software MATLAB package for high throughput ultrasonic vocalizations detection, classification, and analysis.
Proper citation: DeepSqueak (RRID:SCR_021524) Copy
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