KarakulakTulay

Omost

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ComplexHeatmap

Make Complex Heatmaps

gtsummary

Presentation-Ready Data Summary and Analytic Result Tables

scGPT

hexSticker

:sparkles: Hexagon sticker in R

Scientific-Inkscape

Scientific Inkscape: Inkscape extensions for figure resizing and editing

AGAT

Another Gtf/Gff Analysis Toolkit

maftools

Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.

GeneGPT

Code and data for GeneGPT.

immunarch

🧬 Immunarch: an R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires

TransDecoder

TransDecoder source

scCustomize

R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.

copykat

gffcompare

classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF

decoupleR

R package to infer biological activities from omics data using a collection of methods.

TALON

Technology agnostic long read analysis pipeline for transcriptomes

GSoC

Documentation repository of Google Summer of Code (GSoC) project ideas for cBioPortal and related projects

python-package-guide

Scientific Python package recommendations & guidance curated by pyOpenSci

SCEVAN

R package that automatically classifies the cells in the scRNA data by segregating non-malignant cells of tumor microenviroment from the malignant cells. It also infers the copy number profile of malignant cells, identifies subclonal structures and analyses the specific and shared alterations of each subpopulation.

scGate

marker-based purification of cell types from single-cell RNA-seq datasets

TCGAplot

A number of functions were generated to perform pan-cancer DEG analysis, correlation analysis between gene expression and TMB, MSI, TIME, and promoter methylation. Methods for visualization were provided in order to easily perform integrative pan-cancer multi-omics analysis.

CollecTRI

Gene regulatory network containing signed transcription factor-target gene interactions

SCPA

R package for pathway analysis in scRNA-seq data

scATOMIC

Pan-Cancer Single Cell Classifier

orfipy

Fast and flexible ORF finder

single-cell-vocabulary

BRCA-LRseq-pipeline

Pipeline to analyze long-read mRNA isoforms and ORF products sequenced in breast cancer using PacBio Single-Molecule technology.

DIAgui

An interactive shiny app for processing DIA-nn output (filtering, MaxLFQ, Top3, iBAQ, etc.)

scTherapy

Identification of clone-specific and cancer-selective multi-targeting therapeutic options based on single-cell transcriptomic profiles of cancer patients

SplicingFactory

Splicing Diversity Analysis for Transcriptome Data