Precision Health
Precision Health
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RNA Seq Mapping & Assembling
Reads mapping is usually the first step of deep sequencing data analysis. Based on the deep sequencing technology, reads generated by RNA-Seq has similar properties with DNA reads generated by genome re-sequencing in terms of length, quantity, quality and other aspects. For example, they both have the short length, large quantities, uneven quality and high error rates.
However, the RNA-Seq sequencing data also has its own characteristics because it’s from the RNA transcript. Specifically, in the process of transcription from DNA to mRNA, introns are cut out and exons are ligated together in the splicing sites. For the reads across the splicing sites, also known as junction reads, if you don’t break them from the middle, they will not be accurately mapped to the genome.
Переглядів: 2 588

Відео

An Overview of Transcriptome
Переглядів 17 тис.3 роки тому
Transcriptome is the set of all transcripts in a given type of cells. In other words, it is a snapshot of expression profile at a given time of cells. In transcriptome, there are not only the classical messenger RNAs (mRNAs) coding for proteins, but also microRNAs, long non-coding RNAs and other non-coding RNAs recently discovered that do not code for proteins. These RNA transcripts cooperate t...
Determining the Association between Target Gene Expression and Protein Expression of other Genes
Переглядів 4803 роки тому
Determining the Association between Target Gene Expression and Protein Expression of other Genes
Determining the Association of Target Gene Expression and Clinicopathological Characteristics
Переглядів 4193 роки тому
Determining the Association of Target Gene Expression and Clinicopathological Characteristics
Determining the Association between Target Gene Expression and mRNA Expression of other Genes
Переглядів 6003 роки тому
Determining the Association between Target Gene Expression and mRNA Expression of other Genes
Exploring Association of Gene Expression with Clinicopathological Characteristics
Переглядів 3643 роки тому
Exploring Association of Gene Expression with Clinicopathological Characteristics
Metastasis suppressor genes PDAC
Переглядів 1713 роки тому
Metastasis suppressor genes PDAC
EDUCORES - User Guides
Переглядів 2543 роки тому
EDUCORES - User Guides
EDUCORES - Introduction
Переглядів 2003 роки тому
EDUCORES - Introduction
PROVEAN (Protein Variation Effect Analyzer)
Переглядів 2,4 тис.3 роки тому
PROVEAN was developed to predict whether a protein sequence variation affects protein function. PROVEAN is able to provide predictions for any type of protein sequence variations including single or multiple amino acid substitutions, single or multiple amino acid insertions, single or multiple amino acid deletions
Genetic Variant Databases
Переглядів 3,2 тис.3 роки тому
Databases not only allow easy access to large amount of information but also provide data for training machine learning methods and for mining genome wide statistical patterns. Most of the databases of genetic variations were created in the past three decades.
Inherited vs Acquired Mutations
Переглядів 2,7 тис.3 роки тому
Gene mutations can be either inherited or acquired. Inherited mutations are called germline mutations and acquired mutations are called somatic mutations. Somatic mutations or acquired mutations happen when genes mutate over a person's lifetime and are present in the tumor.
PolyPhen-2 (Polymorphism Phenotyping)
Переглядів 4,9 тис.3 роки тому
PolyPhen-2 is an automatic tool for prediction of the possible impact of an amino acid substitution on the structure and function of a human protein. Automated predictions of this kind are essential for interpreting large datasets of rare genetic variants, which have many applications in modern human genetics research. Uses in recent research include identifying rare alleles that cause Mendelia...
SIFT (Sort Intolerant From Tolerant)
Переглядів 2,5 тис.3 роки тому
What features differentiate disease-causing missense SNVs from neutral ones? How can we use these features to predict whether a missense SNV is disease-causing or not? Instead of working with nucleotide changes, almost all the prediction methods of missense variations work directly on the amino acid changes.
Functional Prediction of Genetic Variants
Переглядів 1,9 тис.3 роки тому
Each person's genome has about three million single nucleotide variations, as well as many other types of genetic variations. How do we predict the function of these genetic variations?
Comparing gene expression between normal vs tumor tissues
Переглядів 8943 роки тому
Comparing gene expression between normal vs tumor tissues
Downloading TCGA dataset from GDAC Firehose
Переглядів 1,7 тис.3 роки тому
Downloading TCGA dataset from GDAC Firehose
Identifying Tumor Normal Matched Samples in TCGA
Переглядів 1,5 тис.3 роки тому
Identifying Tumor Normal Matched Samples in TCGA
CMap Analysis - Candidate Therapeutic Discovery Based on Disease-Drug Transcriptomic Similarity
Переглядів 2,5 тис.3 роки тому
CMap Analysis - Candidate Therapeutic Discovery Based on Disease-Drug Transcriptomic Similarity
CMap Analysis - Drug Repurposing Based on Drug-Drug Transcriptomic Similarity
Переглядів 2,2 тис.3 роки тому
CMap Analysis - Drug Repurposing Based on Drug-Drug Transcriptomic Similarity
ConnectivityMap (CMap)
Переглядів 2,7 тис.3 роки тому
ConnectivityMap (CMap)
Drug Gene Interactome and Signature Resources
Переглядів 1,1 тис.3 роки тому
Drug Gene Interactome and Signature Resources
Cancer Pharmacogenomics and System Biology Resources
Переглядів 6763 роки тому
Cancer Pharmacogenomics and System Biology Resources
Cancer Panomics Data Resources
Переглядів 1133 роки тому
Cancer Panomics Data Resources
Drug Repositioning
Переглядів 4273 роки тому
Drug Repositioning
Introduction to Computational Drug Repositioning
Переглядів 3713 роки тому
Introduction to Computational Drug Repositioning
Species Comparison and Tissue Distribution Analysis in Reactome
Переглядів 1793 роки тому
Species Comparison and Tissue Distribution Analysis in Reactome
Analyzing Gene List in Reactome
Переглядів 2,8 тис.3 роки тому
Analyzing Gene List in Reactome
Analyzing Gene Expression in Reactome
Переглядів 1,6 тис.3 роки тому
Analyzing Gene Expression in Reactome
Reactome Analysis Tools
Переглядів 1,3 тис.3 роки тому
Reactome Analysis Tools

КОМЕНТАРІ

  • @dragon5064
    @dragon5064 Рік тому

    .

  • @DB-kv3wu
    @DB-kv3wu Рік тому

    Best tutorial.

  • @zenozeng9441
    @zenozeng9441 Рік тому

    may I ask why change from log2 to normal scale before conducting DEG, thank you! I heard the opposite way

  • @Elonmuskasseater69
    @Elonmuskasseater69 Рік тому

    Interesting

  • @NeelamTripathi-u8q
    @NeelamTripathi-u8q Рік тому

    Thanks for such an informative video I found this more sensible than other videos in UA-cam.

  • @samson_dr
    @samson_dr Рік тому

    Quite informative

  • @afreenjasim7745
    @afreenjasim7745 Рік тому

    This is so helpful! thank you so much!

  • @sinugeorge9485
    @sinugeorge9485 Рік тому

    How to download a controlled dataset?

  • @lukaschumchal7797
    @lukaschumchal7797 Рік тому

    Amazing video. Only missing explanation of HDIV and HVAR to perfection.

  • @sush8926
    @sush8926 Рік тому

    What if not followed?

  • @kiplimosimon1429
    @kiplimosimon1429 Рік тому

    Excellent work

  • @YasminAzaadeh
    @YasminAzaadeh Рік тому

    Great video!

  • @LordBurningStuff
    @LordBurningStuff Рік тому

    Let me be the first. Great video, well explained for a lay man like me.

  • @payalpatel6897
    @payalpatel6897 Рік тому

    thank you so much .

  • @Dr.anonymous-k3m
    @Dr.anonymous-k3m Рік тому

    Although some believe that genetics are just a part of the whole when it comes to human health, I see the future of genomic sequencing as perhaps more prominent in the picture of one’s health profile. Although we are currently limited by many of the technological shortcomings of this new technology, once we have a stronger database and understanding of its significance, I believe this field of medicine will trump all others. When a patient goes to a health care provider, they are advised on different ways in which they can improve the outcome of a particular aspect of their life. With this advice they are working on modifiable lifestyle habits that can benefit them based off knowledge that has worked for health on a large population scale. The advice given to anyone patient is like that to be given to another. The reason I believe that power of genomic counseling potentially underestimated is that it contains the secrete to the undermining unmodifiable factors that a person dealt. Genomics give insights to health advise that is personalized and I believe better for the individual. For instance, perhaps a person has a genetic disposition for hypotension, and they are advised to eat a diet with a higher salt intake. I used an example of a measurement (blood pressure) that falls on a spectrum. I did this because I believe that with the improvement of this technology, we will be able to not only find disease that have a label, but can also give important health advice that can guide the individuals health choices throughout their lives. This would contrast with what most people would be told by their physician, a low sodium diet. Although there are issues with genomics and how they will clash with the social world in the future, I believe that they are the future of health. I believe that the matter of how we can protect one genomic profile is a more important issue as opposed to if we should obtain it.

  • @priscilamenezesmachado4009

    Thank you for share!

  • @kellythayer4970
    @kellythayer4970 Рік тому

    I'd be very interested in seeing a video about how to implement a profile HMM using multinomial profile HMM in scikit learn. If you have such a video please send the link!

  • @shawnkane2138
    @shawnkane2138 2 роки тому

    Thank you so much, learned a lot from your videos.

  • @shawnkane2138
    @shawnkane2138 2 роки тому

    Great video, thanks

  • @shawnkane2138
    @shawnkane2138 2 роки тому

    Awesome, thank you so much!

  • @shawnkane2138
    @shawnkane2138 2 роки тому

    Wonderful!👍 Thank you so much.🙏 🌹

  • @jfaulkner5881
    @jfaulkner5881 2 роки тому

    👍

  • @doomvboom
    @doomvboom 2 роки тому

    How do you calculate the efficiency? What is the -1-10*

  • @ricodsanchez6792
    @ricodsanchez6792 2 роки тому

    nice video

  • @aaronkoh4567
    @aaronkoh4567 2 роки тому

    Hi, could i just ask, If a researcher is concerned about whether an experimental group will be susceptible to more risks when participating in a study than a control group, which ethical principle is the researcher concerned with? Is it the principle of beneficence or that of Justice?

  • @tanyadutta9824
    @tanyadutta9824 2 роки тому

    This is a really informative video if someone wishes to learn in detail about the HUMAN GENOME PROJECT. I am impressed with the animations and the explanations along with the examples. I completely understood HGP after seeing this video. THANK YOU!!

  • @lukewei4758
    @lukewei4758 2 роки тому

    Great video👍

  • @thanayuthchatskulwong8079
    @thanayuthchatskulwong8079 2 роки тому

    Dear sir, For the Effect Data, can I use IC50 values or do I have to use EC50?

  • @ayushanand18
    @ayushanand18 2 роки тому

    Very good and crisp video. Cheers!

  • @husnianurlizt7731
    @husnianurlizt7731 2 роки тому

    Thank you for uploading about drug combination sir, it helped me to understand what my lecturer said ^^

  • @Strawberry_anxiety
    @Strawberry_anxiety 2 роки тому

    👍

  • @blacked2987
    @blacked2987 2 роки тому

    0 14

  • @86harbhajan
    @86harbhajan 2 роки тому

    Excellent 👌

  • @annako22
    @annako22 2 роки тому

    thx man!

  • @gallici-anima-christiana
    @gallici-anima-christiana 2 роки тому

    Thank you, I've started an online course on epigenetics with almost no background so it helps a lot!

  • @weshendrikx9754
    @weshendrikx9754 2 роки тому

    great video thanks

  • @brajmohanr.narayan1254
    @brajmohanr.narayan1254 2 роки тому

    Nice explanation! Thank you very much!

  • @iwannavomit
    @iwannavomit 2 роки тому

    In what situation would one not have a reference sequence?

    • @johnw4727
      @johnw4727 Рік тому

      A lot of marine applications and sequencing of animals in the ocean would not have a reference

  • @ireneyeboah5680
    @ireneyeboah5680 2 роки тому

    Great video! Kindly make a video of how to do it in R or share links to any material of it in R

  • @bangscience6592
    @bangscience6592 2 роки тому

    Thanks. Your vides are very useful. Where can I find a similar dataset with genes? Thanks

  • @NicholeRojas-r8i
    @NicholeRojas-r8i 2 роки тому

    Is it possible to label some genes on excel?

  • @siripichandu7989
    @siripichandu7989 2 роки тому

    😍

  • @marianodanielelean9039
    @marianodanielelean9039 2 роки тому

    Can you provide the cite of the method?

  • @siwakornpunyawatthananukoo6445
    @siwakornpunyawatthananukoo6445 2 роки тому

    Very informative and concise. Thanks you!

  • @kartiknagpal8404
    @kartiknagpal8404 2 роки тому

    How to get this ppt

  • @arghaghosh4113
    @arghaghosh4113 2 роки тому

    Great video! Thanks! What determines what my x-axis values would be? My values seem to be scattered along the x-axis. Is there a way that I can align them in a line?

  • @jenniferwalker1301
    @jenniferwalker1301 2 роки тому

    This video has great information, but the grammar errors make the audio narrative distracting and incorrect. It appears that the computer narration was not developed to pronounce scientific terms (AUG - methionine, start codon, NOT August) and the typed text contains numerous grammatical errors (subject verb agreement, singular plural word usage) that when translated to speech detract from the scientific content.

  • @redbird6622
    @redbird6622 2 роки тому

    Trying to learn this on my own is a bit difficult but not impossible 🙂

  • @tingyanwang294
    @tingyanwang294 2 роки тому

    Very impressive introduction!!

  • @hlatywayowayne2362
    @hlatywayowayne2362 2 роки тому

    Thanks 👍🇿🇼