quantification

There are 2 repositories under quantification topic.

COMBINE-lab / salmon
🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
quasi-mapping bioinformatics rna-seq rnaseq salmon quantification sailfish c-plus-plus gene-expression scrna-seq single-cell 10x selective-alignment rna-seq-quantification single-cell-rna-seq transcriptome
Language:C++ 728
pinellolab / CRISPResso2
Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments
genome-editing quantification amplicon-sequences
Language:Python 251
diplib
DIPlib / diplib
Quantitative Image Analysis in C++, MATLAB and Python
quantitative-image-analysis image-analysis image-processing mathematical-morphology filtering quantification image-viewer cpp cpp14 matlab python python3 bio-formats dipimage diplib
Language:C++ 206
COMBINE-lab / alevin-fry
🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.
single-cell rust transcriptomics rna-seq single-cell-rna-seq quantification 10x
Language:Rust 149
theislab / kBET
An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
data-science batch-effects scrnaseq quantification
Language:HTML 144
rajewsky-lab / mirdeep2
Discovering known and novel miRNAs from small RNA sequencing data
mirna microrna smallrna sequencing analysis prediction quantification mapping
Language:Perl 130
PaulingLiu / ROGUE
Assessing the purity of single cell population
quantification scrna-seq purity clustering
Language:R 79
HLT-ISTI / QuaPy
A framework for Quantification written in Python
machine-learning quantification supervised-prevalence-estimation
Language:Python 56
microsoft / PullRequestQuantifier
A highly customizable framework to quantify a pull request within a repository context.
pull requests quantification size
Language:C# 53
MannLabs / directlfq
Fast and accurate label-free quantification for small and very large numbers of proteomes
algorithms alphapept-ecosystem bioinformatics proteomics python quantification
Language:Jupyter Notebook 32
xu-peng-tao / SSD-Pruning-and-quantization
Pruning and quantization for SSD. Model compression.
ssd prune pruning quantization quantification compression pytorch
Language:Python 27
iquasere / reCOGnizer
A tool for domain based annotation with databases from the Conserved Domains Database
cog-assignment annotation protein fasta quantification genomics functional-annotation
Language:HTML 25
elliotekj / DeltaE
DeltaE is a pure-Rust implementation of the CIEDE2000 algorithm
color quantification cie ciede2000 rust
Language:Rust 24
songjian / cnstats
获取**国家统计局网站数据。
python quantification stats
Language:Python 24
DATASET_PLATEUN01
shm-unesp / DATASET_PLATEUN01
CONCEPT is a dataset of lamb-wave measured in composite structures in healthy and damaged states. This experiment was conducted at the SHM Lab from UNESP Ilha Solteira.
pzt structures damage detection quantification smart-structures lamb-wave structural-health-monitoring delamination
Language:Jupyter Notebook 21
lweasel / piquant
A pipeline to assess the quantification of transcripts.
bioinformatics quantification rna-sequencing transcripts
Language:Python 19
PavlidisLab / rnaseq-pipeline
RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.
rna-seq alignment quantification ngs ngs-analysis illumina rsem star stringtie fastqc bioinformatics-pipeline bioinformatics gene-expression transcriptomics genomics spliced-alignment splice-aware bash
Language:Python 19
smith-chem-wisc / FlashLFQ
Ultra-fast label-free quantification algorithm for mass-spectrometry proteomics
chemistry mass-spectrometry proteomics quantification
Language:C# 18
bkrem / quanti-team
:link: A TenderMint blockchain API to make collaborative work measurable & quantifiable
blockchain tendermint quantification proof-of-concept collaboration paper
Language:JavaScript 16
nf-core / dualrnaseq
Analysis of Dual RNA-seq data - an experimental method for interrogating host-pathogen interactions through simultaneous RNA-seq.
dualrna-seq host-pathogen nextflow nf-core pipeline quantification readmapping rna-seq workflow
Language:Nextflow 16
comprna / ORQAS
ORF Quantification pipeline for Alternative Splicing
ribo-seq translation quantification differential-splicing-analysis
Language:Python 15
nf-core / metaboigniter
Pre-processing of mass spectrometry-based metabolomics data with quantification and identification based on MS1 and MS2 data.
identification mass-spectrometry metabolomics ms1 ms2 nextflow nf-core pipeline quantification workflow
Language:Nextflow 15
smith-chem-wisc / ProteoformSuite
Construction, quantification, and visualization of proteoform families
visualization quantification proteome cytoscape proteoform proteoform-families ptm
Language:C# 11
AICGijon / quantificationlib
QuantificationLib is an open-source library for quantification learning.
machine-learning prevalence-estimation python quantification
Language:Python 10
cpanse / protViz
Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics
cran fun mass-spectrometry peptide-identification proteomics quantification rstats visualization
Language:R 10
ElisabethKugler / ZFVascularQuantification
#ZVQ - Zebrafish Vascular Quantification - https://doi.org/10.1242/dev.199720
segmentation image-processing zebrafish vasculature registration quantification fiji-macro-language fiji openscience lightsheet microscopy microscopy-data
Language:ImageJ Macro 10
mchevalier2 / crestr
A R package to apply the climate reconstruction CREST.
climate taxa crest reconstruction palaeoclimate quantification
Language:R 9
erdogant / flameplot
flameplot is a python package for the quantification of local similarity across two maps or embeddings.
dimensionality-reduction embeddings high-dimensional pca python quantification tsne umap
Language:Python 8
rohitsuratekar / CardioPipeLine
Pipeline for RNA-seq analysis
rna-seq ngs deseq2-analysis quantification pipeline ncbi sra
Language:Python 7
Cai-Lab-at-University-of-Michigan / nGauge
A Python library which provides a collection of tools for the measurement, quantification, and visualization of neuron morphology.
neuron-morphology visualization python-library quantification measurement
Language:Jupyter Notebook 5
jsugarelli / quantification
Quantification of qualitative survey data
carlson-parkin quantification r-package survey survey-analysis survey-data
Language:R 5
snimmagadda1 / PD-and-ET-Tremor-Quantification
🏥 Quantification of Parkinsonian and Essential Tremor using a novel, bluetooth-integrated accelerometer based system
quantification parkinson duke-university wearable wearable-devices bluetooth microcontroller pic
Language:Python 5
sulaimanvesal / CardiacQuanNet
[IEEE-JBHI 2020] TensorFlow/Keras implementation: Spatio-temporal Multi-task Learning for Cardiac MRI Left Ventricle Quantification
deep-learning cardiac-segmentation quantification multitask-learning regression-analysis temporal-le
5
vcangadi1 / EELSAnalyser
EELSAnalyser is a EELS data analysis tool written in MATLAB. Contact : Veer.Angadi@brunel.ac.uk
eels-spectrum-image eels-data eels-si quantification visualization matlab eels energy-loss-axis
Language:MATLAB 5
GliaMorph
ElisabethKugler / GliaMorph
#GliaMorph - Toolkit to Process and Analyse Müller Glia Morphology
zebrafish glia quantification microscopy segmentation microscopy-data comparability openscience fiji fiji-macro-language fiji-macro opensource
Language:ImageJ Macro 4
SBCSnicholsLab / pseudogene_quantification
Repo accompanying our manuscript on quantifying extra-nuclear inserts from population-level low-pass sequencing data
bioinformatics genome-skimming numts nupts pseudogenes quantification wolbachia
Language:Shell 4

quantification

COMBINE-lab / salmon

pinellolab / CRISPResso2

DIPlib / diplib

COMBINE-lab / alevin-fry

theislab / kBET

rajewsky-lab / mirdeep2

PaulingLiu / ROGUE

HLT-ISTI / QuaPy

microsoft / PullRequestQuantifier

MannLabs / directlfq

xu-peng-tao / SSD-Pruning-and-quantization

iquasere / reCOGnizer

elliotekj / DeltaE

songjian / cnstats

shm-unesp / DATASET_PLATEUN01

lweasel / piquant

PavlidisLab / rnaseq-pipeline

smith-chem-wisc / FlashLFQ

bkrem / quanti-team

nf-core / dualrnaseq

comprna / ORQAS

nf-core / metaboigniter

smith-chem-wisc / ProteoformSuite

AICGijon / quantificationlib

cpanse / protViz

ElisabethKugler / ZFVascularQuantification

mchevalier2 / crestr

erdogant / flameplot

rohitsuratekar / CardioPipeLine

Cai-Lab-at-University-of-Michigan / nGauge

jsugarelli / quantification

snimmagadda1 / PD-and-ET-Tremor-Quantification

sulaimanvesal / CardiacQuanNet

vcangadi1 / EELSAnalyser

ElisabethKugler / GliaMorph

SBCSnicholsLab / pseudogene_quantification