User: Kamil

gravatar for Kamil
Kamil2.0k
Reputation:
2,010
Status:
Trusted
Location:
Baltimore
Website:
http://slowkow.com/
Twitter:
slowkow
Scholar ID:
Google Scholar Page
Last seen:
5 days, 1 hour ago
Joined:
10 years, 2 months ago
Email:
k***********@gmail.com

Posts by Kamil

<prev • 97 results • page 1 of 10 • next >
4
votes
6
answers
1.0k
views
6
answers
Answer: A: Rust or C++, what to learn after Go for high-performance bioinformatics tools?
... If you're interested in performance, benchmarks, and language comparisons, you might be interested to read this post by Heng Li: - https://lh3.github.io/2020/05/17/fast-high-level-programming-languages The post has a few benchmarks comparing popular languages: Rust, C, Crystal, Nim, Julia, Python ...
written 5 days ago by Kamil2.0k
0
votes
7
answers
347
views
7
answers
Comment: C: file and directory management best practices
... This seems like a very clever and flexible way to keep notes. Could I please ask where you store the contents of the Wordpress blog? Is it private only to you on your own machine? Have you found a way to share some content with collaborators? ...
written 9 weeks ago by Kamil2.0k
5
votes
0
answers
1.3k
views
0
answers
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 3.1 years ago by Kamil2.0k
0
votes
0
answers
14k
views
0
answers
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 3.1 years ago by Kamil2.0k
1
vote
3
answers
20k
views
3
answers
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 3.8 years ago by Kamil2.0k
1
vote
3
answers
20k
views
3
answers
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 3.8 years ago by Kamil2.0k
1
vote
2
answers
28k
views
2
answers
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 4.0 years ago by Kamil2.0k
0
votes
3
answers
2.5k
views
3
answers
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 4.0 years ago by Kamil2.0k • updated 2.1 years ago by RamRS30k
1
vote
2
answers
4.9k
views
2
answers
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 4.0 years ago by Kamil2.0k
1
vote
5
answers
2.9k
views
5
answers
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 4.5 years ago by Kamil2.0k

Latest awards to Kamil

Scholar 12 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 12 months ago, created an answer that has been accepted. For A: PWM Scan For Toxoplasma gondii
Scholar 12 months ago, created an answer that has been accepted. For A: PWM Scan For Toxoplasma gondii
Great Question 18 months ago, created a question with more than 5,000 views. For FASTA and FASTQ tools
Teacher 18 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 2.3 years ago, created a question with more than 5,000 views. For FASTA and FASTQ tools
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
Appreciated 2.9 years ago, created a post with more than 5 votes. For A: count the number of transcription factor binding sites
Good Answer 2.9 years ago, created an answer that was upvoted at least 5 times. For A: Calculating TPM from featureCounts output
Appreciated 2.9 years ago, created a post with more than 5 votes. For A: count the number of transcription factor binding sites
Teacher 3.1 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 3.1 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 3.1 years ago, created a comment with at least 3 up-votes. For C: Tutorials for Library Normalization in DESeq2 and EdgeR
Librarian 3.1 years ago, created a post with more than 10 bookmarks. For FASTA and FASTQ tools
Appreciated 3.1 years ago, created a post with more than 5 votes. For A: count the number of transcription factor binding sites
Teacher 3.5 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 3.5 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 3.5 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 3.6 years ago, created a question with more than 1,000 views. For Quick statistics from the command line
Scholar 3.7 years ago, created an answer that has been accepted. For A: PWM Scan For Toxoplasma gondii
Teacher 3.8 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 3.9 years ago, created a question with more than 1,000 views. For Quick statistics from the command line
Appreciated 4.0 years ago, created a post with more than 5 votes. For A: count the number of transcription factor binding sites
Popular Question 4.1 years ago, created a question with more than 1,000 views. For Quick statistics from the command line

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1531 users visited in the last hour