Manoj Kumar Valluru's repositories
awesome-pipeline
A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin
bcbio-nextgen
Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
bhtsne
Barnes-Hut t-SNE
biojupies
Automated generation of tailored bioinformatics Jupyter Notebooks via a user interface.
cloudbiolinux
CloudBioLinux: configure virtual (or real) machines with tools for biological analyses
common-workflow-language
Repository for the CWL standards. Use https://www.biostars.org/t/cwl/ for support 😊
cwl-website
www.commonwl.org
DeepPATH
Classification of Lung cancer slide images using deep-learning
deepvariant
Google's DeepVariant variant caller as a Nextflow pipeline
EnhancedVolcano
Publication-ready volcano plots with enhanced colouring and labeling
guessing_game
UNIX WORKBENCH Peer-graded Assignment
hpcuk-website
Source for the HPC-UK website
iCLIPlib
Tools for dealing with iCLIP data
igv
Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
IsoformSwitchAnalyzeR
An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
keras-gcnn
Roto-reflection equivariant CNNs for Keras as presented in B. S. Veeling, J. Linmans, J. Winkens, T. Cohen, M. Welling. "Rotation Equivariant CNNs for Digital Pathology".
lncpipe
UNDER DEVELOPMENT--- A Nextflow-based pipeline for comprehensive analyses of long non-coding RNAs from RNA-seq datasets
Multicore-TSNE
Parallel t-SNE implementation with Python and Torch wrappers.
pandas
Flexible and powerful data analysis / manipulation library for Python, providing labeled data structures similar to R data.frame objects, statistical functions, and much more
parliament2
Runs a combination of tools to generate structural variant calls on whole-genome sequencing data
pathology-images-analysis-using-CNN
Scripts for https://www.nature.com/articles/s41598-018-27707-4, using Convolutional Neural Network to detect lung cancer tumor area
RainCloudPlots
Code and tutorials to visualise your data that is both beautiful *and* statistically valid
raw
The missing link between spreadsheets and data visualization
ReproduciblePython
Workshop materials for PyCon 2018 workshop on reproducible analysis in Python
rna-seq-pipeline
WDL_RNA-Seq_star_rsem
rnafusion
RNA-seq analysis pipeline for detection gene-fusions
the-unix-workbench
:house_with_garden: A Book for Anyone to Get Started with Unix
toil
A scalable, efficient, cross-platform and easy-to-use workflow engine in pure Python
TPMCalculator
TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files