Session 11

In this session, we discussed about the following topics;
– find data
– prepare and process data
– plan analysis
– present findings

Session 10

In this session, we discussed about the following topics;

~ScRNA data analysis, Publication & projects: Drop-seq data from Ye et al., 2017, Results & Interpretation.

Session 10

In this session, we discussed about the following topics;

~ScRNA data analysis, Publication & projects: Drop-seq data from Ye et al., 2017, Results & Interpretation.

Great question! I’ll try to answer the best I can…

Kallisto was published in 2016, which is sort of recent, comparatively. This also suggests that it has been less validated – again, comparatively based on the citations.

Here are some publications on Kallisto

https://www.nature.com/articles/nbt.3519

Here’s one that did a comparison of…[Read more]

Session 9

In this session, we discussed about the following topics;
~Single-cell transcriptomics (SCT) Introduction to SCT, History of SCT, NGS Techniques, Capture techniques, Quantification, scRNA-seq data preparation & Counts

Session 8

In this session we will talk about the following topics:

~Discriminant Analysis and Support Vector Machines
~Feature Selection and expanding the list of features
~Data Visualization

Session 7

In this session we talked about the following topics:

Discriminant Analysis and Support Vector Machines
Feature Selection and expanding the list of features
Data Visualization

Session 6

In this session we talked about the following topics:

Supervised Machine learning techniques
Factor Regression Analysis, Decision Trees, Random Forest
Challenges associated with different kinds of machine learning

Session 5

In today’s session we will talk about the following topics:

~Unsupervised machine learning (PCA, H-Clust, K-means)
~Clustering of samples using gene expression profiles
~Clustering of genes by expression profiles across samples

Visit the Organization Page for more Updates:…[Read more]

Session 4

In this session the following topics were discussed:

~Filtering, removing noise and Normalization Techniques
~Correlation – detecting correlation of features and factors
~Regression, factors, and features – Factor Regression Analysis overview

Session 3

In this session we discussed about the following topics:

~Quantification and Generating a table of expression: RSEM, HTSeq, and Sailfish
~Case study & Hands-on using Cell line project
~Case study & Hands-on using Angelman Project

Visit the Organization Page for more Updates:…[Read more]

Session 2

In Session 2 of the OmicsLogic Transcriptimics Program, we looked at the following topics:
~Role of pre-processing in standard RNA-seq pipelines (Trimmomatic and PCR-clean)
~Mapping techniques: mapping on the transcriptome, mapping on the genome and combined strategies (Bowtie, BWA, and…[Read more]