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142 results • Page 2 of 3
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3.3k
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Tutorial: Applying machine learning to NGS transcriptomic data
next-gen RNA-Seq
updated 11 months ago by 43k • written 6.0 years ago by ▴ 340
2
votes
0
replies
3.2k
views
Tutorial: use the tool slicer to split big files (like FASTQ) to smaller files for parallel processing
opengene slicer fastq splitter
updated 10 months ago by 43k • written 6.5 years ago by ★ 2.5k
2
votes
0
replies
3.2k
views
Tutorial: How to read multiple matrices from GEO into R and make multiple Seurat objects and merge them into a single object.
unix Seurat single-cell rstats
updated 9 months ago by 43k • written 9 months ago by ★ 3.9k
0
votes
1
reply
3.2k
views
Tutorial: Accessing sequences using batch entrez
genome
updated 11 months ago by 43k • written 6.5 years ago by • 0
5
votes
2
replies
3.1k
views
Tutorial: Get GC Content from UCSC with perl script (mysql)
myql ucsc gc-content perl
updated 11 months ago by 43k • written 7.0 years ago by ★ 9.4k
0
votes
0
replies
3.1k
views
Tutorial: Normality Test For JB (Jarque Bera) Test R Commander
Jarque-Bera-Test R-Commander
updated 11 months ago by 43k • written 6.4 years ago by ▴ 10
0
votes
0
replies
2.8k
views
Tutorial: Autocorrelation With Breusch Godfrey Serial Correlation LM Test R Commander
LM-Test R Autocorrelation Breusch-Godfrey
updated 11 months ago by 43k • written 6.4 years ago by ▴ 10
4
votes
2
replies
2.8k
views
Tutorial: Building mosdepth on macOS
nim mosdepth
updated 7 months ago by 141k • written 4.0 years ago by 81k
7
votes
3
replies
2.8k
views
Tutorial: Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation rRNA RNAmmer Genome
updated 4 days ago by 6.4k • written 15 months ago by ▴ 130
2
votes
3
replies
2.7k
views
Tutorial: It's about the journey, and not the destination
R network
updated 11 months ago by 43k • written 7.0 years ago by ★ 1.2k
3
votes
2
replies
2.7k
views
Tutorial: Continuing Education (Pipelines): Best blogs, Online Lectures, Workshops, etc..
conferences Workshops
updated 11 months ago by 43k • written 7.0 years ago by ▴ 100
1
vote
0
replies
2.6k
views
Tutorial: GEO Data Mining (II) - Differential gene expression analysis and visualization with complete code sharing
geo R data-mining differential-gene-expression RNA-Seq
updated 10 months ago by 43k • written 16 months ago by ▴ 420
3
votes
1
reply
2.3k
views
Tutorial: Convert bam files to fastq in numbers as indicated in samtools flagstat stats.
samtools bam alignment fastq sequence
updated 11 months ago by 43k • written 6.9 years ago by ★ 1.6k
4
votes
0
replies
2.3k
views
Tutorial: Accurate prediction of active enhancers using PARE
ChIP-Seq histone-modification enhancer
updated 11 months ago by 43k • written 7.0 years ago by ▴ 100
9
votes
5
replies
2.3k
views
Tutorial: What is new in samtools release 1.5 [Solstice Release] (21st June 2017)
samtools
updated 11 months ago by 43k • written 6.8 years ago by 100k
7
votes
1
reply
2.2k
views
Tutorial: A gentle introduction to biogo
sequence golang biogo
updated 11 months ago by 43k • written 6.5 years ago by ★ 1.7k
3
votes
0
replies
2.2k
views
Tutorial: Deep Learning for Cancer Immunotherapy
keras tensorflow
updated 11 months ago by 43k • written 6.2 years ago by 22k
5
votes
0
replies
2.2k
views
Tutorial: Installing multiprocessor-capable MEME to work with a Slurm job scheduler environment
slurm meme parallel
updated 11 months ago by 43k • written 6.6 years ago by 35k
18
votes
13
replies
2.2k
views
Tutorial: Screen shots of text (please don't)!
meta
updated 11 months ago by 43k • written 7.1 years ago by 54k
0
votes
0
replies
2.2k
views
Tutorial: Transforming (Transformation) Data LN, Log, SQRT In R Commander
R
updated 11 months ago by 43k • written 6.2 years ago by ▴ 10
2
votes
0
replies
2.1k
views
Tutorial: How to display Agilent CGH array in IGV
IGV CGH
updated 11 months ago by 43k • written 6.4 years ago by ★ 2.4k
7
votes
2
replies
1.9k
views
Tutorial: Introduction to Human Genomics for Clinical Informaticists
genome
updated 11 months ago by 43k • written 6.7 years ago by ▴ 90
0
votes
1
reply
1.9k
views
Tutorial: Nonparametric Regression STATA 15
STATA-15 Nonparametric-Regression STATA
updated 11 months ago by 43k • written 6.3 years ago by ▴ 10
4
votes
1
reply
1.9k
views
Tutorial: One of the easy way to achieve read count and RPKM file
RNA-Seq
updated 11 months ago by 43k • written 6.7 years ago by ▴ 40
1
vote
0
replies
1.7k
views
Tutorial: Using Subversion to update /devel branch of Bioconductor package
bioconductor subversion
updated 11 months ago by 43k • written 6.7 years ago by ▴ 350
5
votes
0
replies
1.6k
views
Tutorial: GEO data mining (IB) - Downloading Sequence Read Archive (SRA) raw data
geo RNA-Seq data-mining SRA
updated 10 months ago by 43k • written 16 months ago by ▴ 420
0
votes
0
replies
1.6k
views
Tutorial: PLS SEM (Partial Least Square Sructural Equation Modeling) Analysis WarpPLS 6
R
updated 11 months ago by 43k • written 6.2 years ago by ▴ 10
0
votes
0
replies
1.6k
views
Tutorial: MWD (Mackinnon, White And Davidson) In R
R
updated 11 months ago by 43k • written 6.2 years ago by ▴ 10
2
votes
0
replies
1.5k
views
Tutorial: Webinar: Extracting research evidence from publications
text-mining ontology pubmed
updated 11 months ago by 43k • written 6.1 years ago by ▴ 60
1
vote
2
replies
1.5k
views
Tutorial: ViennaRNA package installation in Windows
windows rna mfold viennarna
updated 10 months ago by 43k • written 19 months ago by ▴ 20
1
vote
0
replies
1.4k
views
Tutorial: Fall 2017 Introduction to Human Genomics for Clinical Informaticists
genome
updated 11 months ago by 43k • written 6.3 years ago by ▴ 90
2
votes
0
replies
1.4k
views
Tutorial: Principal Component Analysis (PCA ON T-BIOINFO)
RNA-Seq next-gen
updated 11 months ago by 43k • written 5.8 years ago by ▴ 340
0
votes
0
replies
1.4k
views
Tutorial: Data Panel In R Commander
R
updated 11 months ago by 43k • written 6.4 years ago by ▴ 10
0
votes
0
replies
1.3k
views
Tutorial: In the cloud - Guide to running VerifyBamID to estimate DNA sample contamination
sequence cloud dna sequencing
updated 11 months ago by 43k • written 5.7 years ago by • 0
2
votes
0
replies
1.2k
views
Tutorial: GEO data mining (III) - Gene pathway enrichment analysis with complete code sharing
geo R data-mining Gene-pathway-enrichment RNA-Seq
updated 10 months ago by 43k • written 16 months ago by ▴ 420
2
votes
0
replies
1.2k
views
Tutorial: Analysis of Smart-Seq3 data with kallisto-bustools
single-cell kallisto transcriptomics smart-seq3 pipeline
updated 5 months ago by • 0 • written 15 months ago by ★ 1.6k
3
votes
3
replies
1.1k
views
Tutorial: multi-omics data integration: a case study with transcriptomics and genomics mutation data
mutation RNAseq multiomics
updated 3 months ago by ▴ 40 • written 8 months ago by ★ 3.9k
8
votes
2
replies
1.1k
views
Tutorial: Updated List of Unix tutorials 2023
Unix
updated 8 months ago by 43k • written 8 months ago by ★ 2.5k
4
votes
2
replies
1.1k
views
Tutorial: How to use UCSC genome browser to check the transcription factor binding at your favorite gene
UCSC transcription factor ChIP-seq
9 months ago by Ming Tommy Tang ★ 3.9k
5
votes
13
replies
1.0k
views
Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R Ubuntu Linux Bioconductor Rstudio
updated 2 days ago by 81k • written 3 days ago by ★ 1.7k
4
votes
0
replies
948
views
Tutorial: How to make a heatmap in R and deep understand it
heatmap r
11 months ago by Ming Tommy Tang ★ 3.9k
1
vote
2
replies
868
views
Tutorial: How to ask computational biology questions
computational-biology
updated 10 months ago by 43k • written 10 months ago by ★ 3.9k
1
vote
0
replies
811
views
Tutorial: List of Machine Learning-Based Scoring Function Papers
machine-learning docking papers
updated 5 months ago by 43k • written 13 months ago by ▴ 10
4
votes
0
replies
765
views
Tutorial: How to do GSEA in R for RNAseq data
gsea RNAseq rstats
9 months ago by Ming Tommy Tang ★ 3.9k
3
votes
0
replies
727
views
Tutorial: best practices for single-cell RNAseq analysis
cell single scRNAseq
10 months ago by Ming Tommy Tang ★ 3.9k
0
votes
4
replies
721
views
Tutorial: Reverse pharmacology: how to predict drugs with genes or disease names?
drugs drug-targets genes
5 months ago by Coremine Medical ▴ 20
2
votes
0
replies
705
views
Tutorial: Get a list of genes associated with a drug in 1 min
drug genes drug-targets
updated 10 months ago by 43k • written 10 months ago by ▴ 20
1
vote
0
replies
680
views
Tutorial: How to pre-process scRNAseq data from fastq to count matrix with two lines of code
unix scRNA-seq single-cell rstats
updated 10 months ago by 43k • written 10 months ago by ★ 3.9k
1
vote
0
replies
679
views
Tutorial: How to convert gene ids in R
computational-biology gene-id rstats
updated 9 months ago by 43k • written 9 months ago by ★ 3.9k
0
votes
0
replies
666
views
Tutorial: T Cell Clonal Analysis Using Single-cell RNA Sequencing and Reference Maps
RNAseq TCR single-cell computational biology
8 months ago by Ming Tommy Tang ★ 3.9k
142 results • Page 2 of 3
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Comment: Correlation for ATAC-Seq and Chip-Seq
Answer: PDB residue serial inconsistency and PDB id&UniProt ID mismatch
Answer: PDB residue serial inconsistency and PDB id&UniProt ID mismatch
Answer: PDB residue serial inconsistency and PDB id&UniProt ID mismatch
Answer: PDB residue serial inconsistency and PDB id&UniProt ID mismatch
Comment: PDB residue serial inconsistency and PDB id&UniProt ID mismatch
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Recent Replies
Answer: WGCNA preservation analysis by Michael 54k
This seems like a model case for why we need better sustainable bioinformatics data and services. I don't know the exact background behind …
Answer: some error in building kraken2 database by Art1ess • 0
this is names.dmp:![names.dmp][1] and nodes.dmp![nodes.dmp][2] [1]: /media/images/33cc9a8b-4818-48b4-913d-1c2b2185 [2]: /media/i…
Comment: Filter BAM to keep only alignments at an interval, ignoring reads spliced over by Pierre Lindenbaum 161k
see also : https://www.biostars.org/p/9537698/ ; https://www.biostars.org/p/9464312/ ; https://www.biostars.org/p/417123/
Comment: Filter BAM to keep only alignments at an interval, ignoring reads spliced over by Pierre Lindenbaum 161k
what's the gray section ? it's the read you want ? do you only want the reads that end at the splice event (single point location) ?
Comment: interpretartion of a vcf file by Pierre Lindenbaum 161k
yes if there is more than one sample genotyped.
Comment: interpretartion of a vcf file by samuelkalandarov2002 ▴ 10
Is it typical to observe such a profile in the context of diploid organism ?
Answer: Plots for DNA methylation data by Basti ★ 2.0k
Yes you can use ggplot2 to create your own plots from a table of results from a differential methylation analysis. You just need to adapt a…
Comment: Heatmap and rna-seq by Basti ★ 2.0k
This forum is not dedicated to this type of request, there are many online tutorials for creating heatmaps accessible with simple internet …
Answer: python file for coding potential calculator by atharvakarkare14 ▴ 10
Download the CPC2 tool supported by python 3 from here [https://github.com/gao-lab/CPC2_standalone/releases/tag/v1.0.1][1]. Then follow …
Comment: Redirection of Duplicate PMIDs by LauferVA 4.2k
let me know the scope and scale of the request (e.g. I need to do this for every record in Pubmed) and can help
Comment: Redirection of Duplicate PMIDs by LauferVA 4.2k
how is this query itself originating?
Comment: Redirection of Duplicate PMIDs by dominickd • 0
I was able to come up with a workaround using the requests library: import requests pmid = 30134295 url = 'https://pubmed.ncbi…
Comment: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks? by HyperEvo • 0
Thanks for you answer! Actually I have already filtered my peak according to blacklist by bedtools. You mean it's meaningless to compare on…
Answer: Redirection of Duplicate PMIDs by GenoMax 141k
More than likely not since the database query seems to work for the redirected PMID but not the original. $ esearch -db pubmed -query …
Comment: DYH17 Structure Prediction by anasjamshed ▴ 120
Blast showed PDB: 8J07_n9(human) as best template with 62.99%. I also used swissmodel to model the protein and it showed: https://swissmod…
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