Pinned Repositories
bioinformatics
:microscope: Path to a free self-taught education in Bioinformatics!
brc-parser
bam-readcount parser
hpackedbubble
Create Split Packed Bubble Charts
kraken-review
🦑 Visualize phylogenetic trees from the taxonomic sequence classifier: Kraken
mxnet
Lightweight, Portable, Flexible Distributed/Mobile Deep Learning with Dynamic, Mutation-aware Dataflow Dep Scheduler; for Python, R, Julia, Scala, Go, Javascript and more
Qiime16sTutorial
A tutorial on up-to-date methods of 16S analysis with QIIME
seurat_docker
docker image seurat
SPLICE-q
SPLICE-q -- A Python tool for genome-wide SPLIcing Efficiency quantification from RNA-seq data.
training-collection
Collection of bioinformatics training materials
sridhar0605's Repositories
sridhar0605/bioinformatics
:microscope: Path to a free self-taught education in Bioinformatics!
sridhar0605/mxnet
Lightweight, Portable, Flexible Distributed/Mobile Deep Learning with Dynamic, Mutation-aware Dataflow Dep Scheduler; for Python, R, Julia, Scala, Go, Javascript and more
sridhar0605/bamclipper
Remove primer sequence from BAM alignments by soft-clipping
sridhar0605/Bash-Oneliner
Bash Oneliner learning station. This blog will focus on bash commands for parsing biological data, which are tsv files(tab-separated values); some of the commands are for Ubuntu system maintaining. I apologize that there won't be any citation of the code, but they are probably from dear Google and Stackoverflow. Not all the code here are oneliner (if the ';' counts..). English and bash are not my first language, so... correct me anytime, tks!!
sridhar0605/bcbb
Incubator for useful bioinformatics code, primarily in Python and R
sridhar0605/bd_python
sridhar0605/biocode
Bioinformatics code libraries and scripts
sridhar0605/bioscripts
scripts I am using on a daily basis
sridhar0605/Clean-code-in-Python
As presented in EuroPython 2016
sridhar0605/containers
Bioinformatics containers
sridhar0605/dash
Interactive, reactive web apps in pure python :star:
sridhar0605/exprAnalysis
exprAnalysis
sridhar0605/iDEP
iDEP: integrated Differential Expression & Pathway analysis
sridhar0605/interval_tree_for_overlaps
sridhar0605/mutation_analysis_scripts
day to day activity for mutation data
sridhar0605/nanostring_validation
markdown file for nanonstring validation
sridhar0605/outrigger
Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data
sridhar0605/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
sridhar0605/picobio
Miscellaneous Bioinformatics scripts etc mostly in Python
sridhar0605/primerDesign
A tool to design highly specific PCR primers for the validation of genomic alterations including structural variants
sridhar0605/pyomics
sridhar0605/PythonDataScienceHandbook
Jupyter Notebooks for the Python Data Science Handbook
sridhar0605/qiime
Quantitative Insights Into Microbial Ecology (QIIME): Official repository for software and unit tests
sridhar0605/rna-seq-qc
Rna-seq pipeline, From FASTQ to differential expression analysis...
sridhar0605/rnaSeqFPro
rnaSeqFPro (beta) is a script for full processing of RNASeq data starting from fastq files. It performs fastqc quality control, mapping to the human genome hg19 using STAR second pass, counting with featurecounts using GENCODE gtf annotation, creates master table, performs differential analysis using DESeq2, generates graphs in gglot2.
sridhar0605/scikit-learn-book
Source code for the "Learning scikit-learn: Machine Learning in Python"
sridhar0605/ScreenProcessing
sridhar0605/single_cell_analysis
Introduction to single-cell RNA-Seq analysis workshop
sridhar0605/spliceR
This is a read-only mirror of the Bioconductor SVN repository. Package Homepage: http://bioconductor.org/packages/devel/bioc/html/spliceR.html Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=spliceR.
sridhar0605/Topsorter
Graphical assessment of structrial variants using 10x genomics data