shrutimarwaha Goto Github PK

bedtools-protocols

bioinformatics-related-r-codes

codes related to bioinformatics tasks

cytof

Analysis of CyTOF data

gastriccancermetaanalysis

find commmon differentially expressed genes among different gastric cancer microarray studies

gse27342_geneexpression_cmap_analysis

Analysis of gene expression data (microarray, GSE27342) to identify differentially expressed genes between tumor and normal tissue. Further use the differentially expressed genes (DEG) to identify potential therapeutic compounds using Connectivity Map (CMap).

gtex-pipeline

GTEx Consortium data production and analysis pipelines

happycompare

Reporting toolbox for happy output

head-neckcancer

Head&NeckCancer repository contains codes for analysis of different Head&NeckCancer datasets

kagglesfcrime

Kaggle Challenge to classify 39 different crimes that occurred in SF in 12 years. https://www.kaggle.com/c/sf-crime

labs

Rmd source files for the HarvardX series PH525x

machinelearning

Machine Learning related R scripts

mimic

Machine Learning Project to analyze data from ICU patients from MIMIC.

mimic-code

MIMIC Code Repository: Code shared by the research community for the MIMIC-III database

ngs_unix

Shell scripts for different tasks for analyzing Next Generation Sequencing (NGS) data

predictsubchains

"You have a chain with links numbered through . Every minute, you draw a random link from a bag, and connect it to any other consecutively­numbered link that you drew before.For example, if you drew , you would end up with three subchains: . You keep on drawing until you have drawn all links and connected them into a single chain of length . Let be the maximum number of subchains in this process. Find what is the mean and standard deviation of the distribution of if = 8 or 16 or 32"

python

Python Codes

qpcr_invitro_experiment

This is an R Markdown document to analyze qPCR data from an experiment which tests if SHH can further enhance the expression of cytokines (IL-12, IL-1β, CXCL-2 and TNF) in H. pylori stimulated macrophages.

qpcr_invivo_experiment

Analysis of qPCR Experiments: Analysis of qPCR data obtained from WT and PC-SHH-KO mice infected with Helicobacter pylori or uninfected. Two types of statistical tests are performed: Interaction plots and Two-way ANOVA.

rcodes

Miscellaneous R codes

rnaseq_analysis_pipeline_on_aws

This repository contains codes that perform Quality Control, Analysis of QC results, Read Mapping, Transcriptome Reconstruction, Differential Expression Analysis and Functional Analysis

sql

SQL related projects

time-series-data

IL-1b, IL-10 and IFNg trajectories in Helicobacter pylori infection. We extracted and analyzed time-series data for IL-10, IFNγ, IL-1β from gse37938 dataset. For a given probe, median of its expression values was calculated for each time point. The median values for both control and H.pylori infection were plotted against time to study their trajectory. Probes with two or more missing values for more than one time point, were ignored. To address the problem of probe selection, median value was taken for probes with same Genbank ID (GB_list ID ) while probes with different Genbank ID were analyzed separately.

wdl

website

Shruti's personal website

worldcuisinedataanalysis

To identify similarity and patterns among different cuisines of the world.