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scCATCHAutomatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
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squidSQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data
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MetaOmGraphMetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets
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IsoQuantReference-based transcript discovery from long RNA read
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TransPiTransPi – a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly
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CICEROCICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data.
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MUMandCoMUM&Co is a simple bash script that uses Whole Genome Alignment information provided by MUMmer (only v4) to detect Structural Variation
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dropClustVersion 2.1.0 released
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picardmetrics🚦 Run Picard on BAM files and collate 90 metrics into one file.
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CD4-csawReproducible reanalysis of a combined ChIP-Seq & RNA-Seq data set
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CoNekTCoNekT (short for Co-expression Network Toolkit) is a platform to browse co-expression data and enable cross-species comparisons.
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civicmineText mining cancer biomarkers for the CIVIC database
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iDEADifferential expression (DE); gene set Enrichment Analysis (GSEA); single cell RNAseq studies (scRNAseq)
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EWCEExpression Weighted Celltype Enrichment. See the package website for up-to-date instructions on usage.
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classifying-cancerA Python-Tensorflow neural network for classifying cancer data
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oncoEnrichRCancer-dedicated gene set interpretation
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Front-EndFederated Learning based Deep Learning. Docs: https://fets-ai.github.io/Front-End/
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RNASeqRNASeq pipeline
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sedefIdentification of segmental duplications in the genome
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svtoolsTools for processing and analyzing structural variants.
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SVCollectorMethod to optimally select samples for validation and resequencing
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FEELncFEELnc : FlExible Extraction of LncRNA
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velodynDynamical systems methods for RNA velocity analysis
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diffexprPorting DESeq2 and DEXSeq into python via rpy2
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rare-disease-wf(WIP) best-practices workflow for rare disease
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tailseekerSoftware for measuring poly(A) tail length and 3′-end modifications using a high-throughput sequencer
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biojupiesAutomated generation of tailored bioinformatics Jupyter Notebooks via a user interface.
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rnafusionRNA-seq analysis pipeline for detection gene-fusions
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gene-oracleFeature extraction algorithm for genomic data
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NGI-RNAseqNextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.
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dammitjust annotate it, dammit!
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cellSNPPileup biallelic SNPs from single-cell and bulk RNA-seq data
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paccmann rlCode pipeline for the PaccMann^RL in iScience: https://www.cell.com/iscience/fulltext/S2589-0042(21)00237-6
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READemptionA pipeline for the computational evaluation of RNA-Seq data
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arcsvComplex structural variant detection from WGS data
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RATTLEReference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing
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DEcodeA prediction model for differential gene expression (DE) based on genome-wide regulatory interactions
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PandoMultiome GRN inference.
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hotspot3d3D hotspot mutation proximity analysis tool
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snakefiles🐍 Snakefiles for common RNA-seq data analysis workflows.
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IARC-nfList of IARC bioinformatics nextflow pipelines
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smartas📓Notebook of Climente-González et al. (2017), The Functional Impact of Alternative Splicing in Cancer.
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slamdunkStreamlining SLAM-seq analysis with ultra-high sensitivity
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cpsrCancer Predisposition Sequencing Reporter (CPSR)
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