User: zhenyisong

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zhenyisong130
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China
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1 year ago
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Posts by zhenyisong

<prev • 28 results • page 2 of 3 • next >
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Comment: C: single cell RNA-seq anlysis, PCA method, how to choose variables which contribut
... I remember that each Principle Component(PC) has its weight. Should we times each weight and compare those four components before selecting the max one? ...
written 4.8 years ago by zhenyisong130
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Comment: C: single cell RNA-seq anlysis, PCA method, how to choose variables which contribut
... I greatly appreciate your help. Thanks again. However, I am wondering if this approach (Option 2) is empirical method or has some convincing reason to do so (reference?)? ...
written 4.8 years ago by zhenyisong130
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Comment: C: single cell RNA-seq anlysis, PCA method, how to choose variables which contribut
... I mean, how the highest PC loadings were calculated? I want to make sure whether "the first three or four" weights are added up and ordered by the sum (row) or single out one largest pc in those four components and then make an order. My understanding is that there are still two possible ways to int ...
written 4.8 years ago by zhenyisong130
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Comment: C: single cell RNA-seq anlysis, PCA method, how to choose variables which contribut
... No. Someone suggested that the first way is OK (add the weights together and then ordering). But I did not find this explanation from the textbook. I wrote a letter to the authors and asked the source code, but no response. Anyway, if you find the answer,do let me know. ...
written 4.8 years ago by zhenyisong130
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PWM matching alogrithm
... I want to optimize the PWM algorithm. My original approach is brute force strategy which each position PWM score is calculated and compared with the threshold.Thus the running time is exponential dependent on the length of input string (DNA fragment). Is there some kind of speeding method to improve ...
alogrithm; ;dna pwm motif written 4.9 years ago by zhenyisong130 • updated 3.8 years ago by ibarra.ignacio10
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Comment: C: Is there any specific quality metrics for lncRNA-seq or miRNA-seq?
... you mean that researchers use the same quality metrics as mRNA-seq? ...
written 5.0 years ago by zhenyisong130
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Is there any specific quality metrics for lncRNA-seq or miRNA-seq?
... I read this thread about RNA-seq data quality control. But for lnc RNA-seq or miRNA-seq, what should we carefully plan in the steps of quality control and preoprocessing before we analyze the data? ...
lncrna-seq small rna-seq sequencing written 5.0 years ago by zhenyisong130 • updated 5.0 years ago by Devon Ryan93k
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single cell RNA-seq anlysis, PCA method, how to choose variables which contribute most to components?
... I read the paper by Quake lab about using single cell RNA-seq to find new cell lineage marker in lung development. Their method is to use PCA (principle component analysis) to  select genes to do unsupervised hierarchical clustering (HC). Here they described that " Genes with highest loadings in the ...
pca written 5.1 years ago by zhenyisong130 • updated 4.8 years ago by Jean-Karim Heriche21k
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Comment: C: where can find the dataset for the genes of fatty acid metabolism?
... Thanks. This is the third way to retrieve the data-set on fatty acid metabolism. My worry is that, I compare those datasets from different sources, they are overlapped but not identical. I want to make sure which one is authoritative and most updated. ...
written 5.1 years ago by zhenyisong130
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Comment: C: where can find the dataset for the genes of fatty acid metabolism?
... thanks. I changed the title. ...
written 5.1 years ago by zhenyisong130

Latest awards to zhenyisong

Teacher 23 months ago, created an answer with at least 3 up-votes. For A: indexed human reference genome
Scholar 23 months ago, created an answer that has been accepted. For A: indexed human reference genome
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Is there any specific quality metrics for lncRNA-seq or miRNA-seq?
Popular Question 2.4 years ago, created a question with more than 1,000 views. For PWM matching alogrithm
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Is there any specific quality metrics for lncRNA-seq or miRNA-seq?

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