User: Kamil

gravatar for Kamil
Kamil2.0k
Reputation:
1,970
Status:
Trusted
Location:
Baltimore
Website:
http://slowkow.com/
Twitter:
slowkow
Scholar ID:
Google Scholar Page
Last seen:
1 month, 1 week ago
Joined:
10 years ago
Email:
k***********@gmail.com

Posts by Kamil

<prev • 95 results • page 1 of 10 • next >
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Comment: C: Tutorials for Library Normalization in DESeq2 and EdgeR
... Also check out Joshua Starmer's other great videos here: https://statquest.org He's done a fantastic job breaking down statistical ideas and explaining them step by step. ...
written 2.9 years ago by Kamil2.0k
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Comment: C: Produce PCA for 1000 Genomes Phase III in VCF format
... Looks nice! Thanks for posting. Could I ask you to please include a PCA figure directly in your post? ...
written 2.9 years ago by Kamil2.0k
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Comment: C: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
... My script expects to read a file compressed with `gzip`, but you provided a decompressed file. Try running `gzip gene2ensembl` and then run the script again. ...
written 3.6 years ago by Kamil2.0k
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Comment: C: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
... I updated the comment in `count_bp` with a visual example of how exons are counted. You can find gene annotations in GTF format for many species here: ftp://ftp.ensembl.org/pub/release-87/gtf/ Note that the version (87 at the time of this post) is continually updated over time. Regarding convert ...
written 3.6 years ago by Kamil2.0k
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Comment: C: Calculating TPM from featureCounts output
... Thanks for the suggestion! I [modified the function][1] for you. [1]: https://gist.github.com/slowkow/c6ab0348747f86e2748b#file-counts_to_tpm-r-L44 ...
written 3.8 years ago by Kamil2.0k
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Comment: C: RNA-seq: differentially expressed genes without genome reference
... Kallisto requires sequencing reads and a file with target sequences. Please see the [kallisto manual][1] for more information. [1]: https://pachterlab.github.io/kallisto/manual ...
written 3.8 years ago by Kamil2.0k • updated 22 months ago by RamRS28k
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Answer: A: Download Transcription Factor Targeting Genes Data
... You might be interested in this R package: https://github.com/slowkow/tftargets It summarizes 6 datasets: * [TRED][tred] (2007) * [ITFP][itfp] (2008) * [ENCODE][encode] (2012) * [Neph2012][neph2012] (2012) * [TRRUST][trrust] (2015) * [Marbach2016][marbach2016] (2016) [tred]: https://github.com/sl ...
written 3.8 years ago by Kamil2.0k
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Answer: A: quantify signal in a chromosomal interval in different .bw files
... ## bigWigToBedGraph Download `bigWigToBedGraph` from: http://hgdownload.cse.ucsc.edu/admin/exe/ You can pass genomic coordinates like this: $ bigWigToBedGraph -chrom=chr1 -start=123 -end=456 input.bw output.bedGraph ## bwtool [Ming Tang](https://twitter.com/tangming2005/status/72515445552449 ...
written 4.3 years ago by Kamil2.0k
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Answer: A: RNA-seq: differentially expressed genes without genome reference
... If you know which transcripts belong to a gene, then you can sum their TPM values to get the gene's TPM. Consider using Kallisto to get quick and accurate results. Next, use your preferred method for [differential expression analysis][1]: limma, DESeq, edgeR, etc. [1]: https://www.bioconductor.o ...
written 4.5 years ago by Kamil2.0k • updated 22 months ago by RamRS28k
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Answer: A: automated gene ontology enrichment for simple gene list (not microarray data)
... You might start by considering a function in the limma package called goana. See the examples in the documentation. The function can perform an enrichment test even if you only provide a vector or Entrez Gene IDs, without any other inputs. See all the other packages available for Gene Set Enrichmen ...
written 4.5 years ago by Kamil2.0k

Latest awards to Kamil

Scholar 9 months ago, created an answer that has been accepted. For A: How to find start and stop codon for sequences in a fasta file?
Scholar 9 months ago, created an answer that has been accepted. For A: PWM Scan For Toxoplasma gondii
Scholar 10 months ago, created an answer that has been accepted. For A: PWM Scan For Toxoplasma gondii
Great Question 15 months ago, created a question with more than 5,000 views. For FASTA and FASTQ tools
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Is There Any Way To Retrieve Protein Sequences In Fasta Format using a Kegg Path
Great Question 2.1 years ago, created a question with more than 5,000 views. For FASTA and FASTQ tools
Good Answer 2.5 years ago, created an answer that was upvoted at least 5 times. For A: Calculating TPM from featureCounts output
Appreciated 2.5 years ago, created a post with more than 5 votes. For A: count the number of transcription factor binding sites
Appreciated 2.7 years ago, created a post with more than 5 votes. For A: count the number of transcription factor binding sites
Good Answer 2.7 years ago, created an answer that was upvoted at least 5 times. For A: Calculating TPM from featureCounts output
Appreciated 2.7 years ago, created a post with more than 5 votes. For A: count the number of transcription factor binding sites
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: Is There Any Way To Retrieve Protein Sequences In Fasta Format using a Kegg Path
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: Is There Any Way To Retrieve Protein Sequences In Fasta Format using a Kegg Path
Commentator 2.9 years ago, created a comment with at least 3 up-votes. For C: Tutorials for Library Normalization in DESeq2 and EdgeR
Librarian 2.9 years ago, created a post with more than 10 bookmarks. For FASTA and FASTQ tools
Appreciated 2.9 years ago, created a post with more than 5 votes. For A: count the number of transcription factor binding sites
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: Is There Any Way To Retrieve Protein Sequences In Fasta Format using a Kegg Path
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: Is There Any Way To Retrieve Protein Sequences In Fasta Format using a Kegg Path
Popular Question 3.3 years ago, created a question with more than 1,000 views. For pytabix - quickly retrieve rows from a table of positions or regions
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Quick statistics from the command line
Scholar 3.5 years ago, created an answer that has been accepted. For A: PWM Scan For Toxoplasma gondii
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: Is There Any Way To Retrieve Protein Sequences In Fasta Format using a Kegg Path
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Quick statistics from the command line
Appreciated 3.8 years ago, created a post with more than 5 votes. For A: count the number of transcription factor binding sites
Popular Question 3.9 years ago, created a question with more than 1,000 views. For Quick statistics from the command line

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