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21
votes
9
replies
6.2k
views
8 follow
Tutorial: Interactive Perl Learning
perl
updated 6 months ago by 40k • written 10.3 years ago by 9.7k
282
votes
39
replies
174k
views
29 follow
Tutorial: How to download raw sequence data from GEO/SRA
fastq SRA bam GEO
updated 6 months ago by 40k • written 9.1 years ago by 20k
64
votes
26
replies
12k
views
7 follow
Tutorial: Parallel processing in R
biocparallel mclapply foreach R
updated 6 months ago by 40k • written 6.0 years ago by 86k
34
votes
15
replies
5.8k
views
6 follow
Tutorial: How to do data cleaning for VCF genetic file
vcf
updated 6 months ago by 40k • written 4.3 years ago by ★ 9.3k
20
votes
4
replies
2.4k
views
Tutorial: Bash One-liners collection on Github
bash linux shell
updated 6 months ago by 40k • written 4.4 years ago by ▴ 180
14
votes
7
replies
5.9k
views
Tutorial: Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
ChIP-Seq peaks R HOMER
updated 6 months ago by 40k • written 7.4 years ago by ★ 3.3k
2
votes
0
replies
4.3k
views
Tutorial: Calculation of TSS Scores for ATAC-seq Data
next-gen-sequencing
updated 6 months ago by 40k • written 4.2 years ago by ▴ 20
0
votes
0
replies
995
views
Tutorial: Apply ALoFT to identify loss-of-function somatic or germline variants
ALoFT
updated 6 months ago by 40k • written 4.3 years ago by ★ 9.3k
16
votes
11
replies
14k
views
7 follow
Tutorial: retrieve full TCGA datasets from cBioportal with R
TCGA RNA-seq data-retrieval cBioportal R
updated 6 months ago by 40k • written 6.9 years ago by ★ 4.7k
10
votes
5
replies
21k
views
Tutorial: Y-DNA and mtDNA Haplogroup Predictor
haplogroup
updated 6 months ago by 40k • written 5.2 years ago by ★ 9.3k
34
votes
15
replies
19k
views
12 follow
Tutorial: TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen GDC R TCGA
updated 6 months ago by 40k • written 7.0 years ago by ▴ 310
6
votes
3
replies
4.3k
views
Tutorial: Principles and Workflow of 16S/18S/ITS Amplicon Sequencing
alignment sequencing RNA-seq gene
updated 6 months ago by 40k • written 4.9 years ago by ▴ 40
0
votes
0
replies
1.0k
views
Tutorial: Introduction to Gen3 Webinar
gen3 open-source data-commons big-data
updated 6 months ago by 40k • written 4.6 years ago by ▴ 310
0
votes
1
reply
1.3k
views
Tutorial: SFA (Stochastic Frontier Analysis) Frontier 4.1
r spss
updated 6 months ago by 40k • written 5.6 years ago by ▴ 10
4
votes
2
replies
3.4k
views
Tutorial: Introduce OpenGene: an open source library for processing NGS data
NGS sequencing Julia OpenGene
updated 6 months ago by 40k • written 7.6 years ago by ★ 2.4k
28
votes
4
replies
4.0k
views
Tutorial: Modern Statistics for Modern Biology
statistics
updated 6 months ago by 40k • written 4.7 years ago by 26k
61
votes
6
replies
9.2k
views
Tutorial: Minimum Standards For Bioinformatics Command Line Tools
command-line
updated 6 months ago by 40k • written 10.1 years ago by 9.7k
4
votes
0
replies
853
views
Tutorial: Finding individual motif occurrences with FIMO from the MEME suite
motif meme jaspar fimo
updated 6 months ago by 40k • written 4.8 years ago by 76k
5
votes
2
replies
2.1k
views
Tutorial: NCBI submissions: SRA and TSA
NCBI TSA SRA RNA-Seq
updated 6 months ago by 40k • written 4.8 years ago by ▴ 50
6
votes
0
replies
1.5k
views
Tutorial: NCBI dbVar releases updated human reference structural variation (SV) data files and tutorials
dbvar structural-variation
updated 6 months ago by 40k • written 4.9 years ago by ▴ 70
32
votes
4
replies
7.0k
views
Tutorial: Fast LD computation from VCF files using tomahawk
ld snp vcf vcftools bcftools
updated 6 months ago by 40k • written 4.9 years ago by ★ 1.6k
58
votes
25
replies
38k
views
15 follow
Tutorial: Protocol To Downlad TCGA Data From GDC
GDC methylation TCGA
updated 6 months ago by 40k • written 7.2 years ago by ★ 9.3k
61
votes
15
replies
13k
views
Tutorial: Which human reference genome should I use?
assembly genome alignment
updated 4 months ago by 40k • written 5.0 years ago by 16k
3
votes
4
replies
3.5k
views
Tutorial: Gene Set Enrichment Analysis on T-BioInfo
gene RNA-Seq
updated 4 months ago by 40k • written 4.9 years ago by ▴ 340
22
votes
2
replies
5.8k
views
Tutorial: Use a workflow management tool to manage your computational pipelines
workflow-management snakemake pipeline
updated 5 months ago by 40k • written 6.9 years ago by ★ 2.1k
1
vote
2
replies
3.1k
views
Tutorial: Standalone BLAST error: UnexpectedTagClassByte
software-error blast
updated 11 months ago by 40k • written 8.1 years ago by ▴ 10
10
votes
4
replies
3.2k
views
Tutorial: CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation corlevelplot
updated 4 months ago by 40k • written 5.6 years ago by 86k
75
votes
13
replies
66k
views
10 follow
Tutorial: Machine Learning For Prediction of Relapse in Cancer - Part 2 - Building A Random Forest Classifier
r cancer classification
updated 10 months ago by 40k • written 9.8 years ago by ★ 1.2k
20
votes
4
replies
14k
views
Tutorial: How To Install A Specific Cdf Package For Use In Bioconductor
bioconductor affymetrix
updated 7 months ago by 40k • written 10.5 years ago by 20k
0
votes
0
replies
1.2k
views
Tutorial: In the cloud - Guide to running VerifyBamID to estimate DNA sample contamination
sequence cloud dna sequencing
updated 4 months ago by 40k • written 5.2 years ago by • 0
20
votes
2
replies
7.6k
views
Tutorial: Creating a karyotype plot with genes using karyoploteR
karyoploteR visualization R genome
updated 4 months ago by 40k • written 5.8 years ago by ★ 3.4k
2
votes
0
replies
1.3k
views
Tutorial: Principal Component Analysis (PCA ON T-BIOINFO)
RNA-Seq next-gen
updated 4 months ago by 40k • written 5.3 years ago by ▴ 340
9
votes
23
replies
9.1k
views
7 follow
Tutorial: OrthoMCL installation on Ubuntu Linux
ubuntu orthomcl mysql linux
updated 4 months ago by 40k • written 5.7 years ago by ▴ 310
1
vote
4
replies
3.1k
views
Tutorial: Applying machine learning to NGS transcriptomic data
next-gen RNA-Seq
updated 4 months ago by 40k • written 5.4 years ago by ▴ 340
3
votes
4
replies
4.2k
views
Tutorial: gencore: a tool to reduce sequencing noises by generating consensus reads
consensus OpenGene sequencing-noise
updated 4 months ago by 40k • written 5.4 years ago by ★ 2.4k
18
votes
2
replies
5.7k
views
Tutorial: Update kraken databases
database kraken k-mer python
updated 4 months ago by 40k • written 6.4 years ago by 5.2k
2
votes
0
replies
1.4k
views
Tutorial: Webinar: Extracting research evidence from publications
text-mining ontology pubmed
updated 4 months ago by 40k • written 5.6 years ago by ▴ 60
146
votes
34
replies
53k
views
17 follow
Tutorial: Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
music cancer tcga mutation maf
updated 7 months ago by 40k • written 10.4 years ago by 6.0k
1
vote
0
replies
2.2k
views
Tutorial: Tutorial DEAP 2.1 In DOS
deap2.1 R
updated 6 months ago by 40k • written 5.6 years ago by ▴ 10
0
votes
0
replies
3.5k
views
Tutorial: SFA (Stochastic Frontier Analysis) STATA 14
R
updated 4 months ago by 40k • written 5.6 years ago by ▴ 10
0
votes
0
replies
1.5k
views
Tutorial: PLS SEM (Partial Least Square Sructural Equation Modeling) Analysis WarpPLS 6
R
updated 4 months ago by 40k • written 5.6 years ago by ▴ 10
3
votes
0
replies
2.1k
views
Tutorial: Deep Learning for Cancer Immunotherapy
keras tensorflow
updated 4 months ago by 40k • written 5.7 years ago by 21k
0
votes
0
replies
1.4k
views
Tutorial: MWD (Mackinnon, White And Davidson) In R
R
updated 4 months ago by 40k • written 5.7 years ago by ▴ 10
0
votes
0
replies
2.1k
views
Tutorial: Transforming (Transformation) Data LN, Log, SQRT In R Commander
R
updated 4 months ago by 40k • written 5.7 years ago by ▴ 10
14
votes
2
replies
2.3k
views
Tutorial: Exploring OpenSNP - an RMarkdown report on crowdsourced genotypes and phenotypes
SNP R
updated 5 months ago by 40k • written 7.5 years ago by 21k
0
votes
0
replies
3.5k
views
Tutorial: Park Test for Heteroskedasticity In R Commander
R Park-Test
updated 4 months ago by 40k • written 5.7 years ago by ▴ 10
0
votes
0
replies
7.8k
views
Tutorial: Multicollinearity VIF (Variance Inflation Factor) Analysis in Panel data EVIEWS 9
R eviews
updated 4 months ago by 40k • written 5.7 years ago by ▴ 10
23
votes
19
replies
6.1k
views
10 follow
Tutorial: MutScan: Detect important mutations by scanning FastQ files directly
fastq mutation cancer target
updated 5 months ago by 40k • written 7.0 years ago by ★ 2.4k
1
vote
0
replies
1.3k
views
Tutorial: Fall 2017 Introduction to Human Genomics for Clinical Informaticists
genome
updated 4 months ago by 40k • written 5.7 years ago by ▴ 90
0
votes
1
reply
1.7k
views
Tutorial: Guide Tutorial DEAP 2.1 In Windows 7
DEAP2.1 R stata
updated 6 months ago by 40k • written 5.7 years ago by ▴ 10
379 results • Page 4 of 8
Recent Votes
Answer: Filter transcription factors
Answer: Filter transcription factors
Answer: Filter transcription factors
Comment: Integrated Seurat object change name of the two conditions
Comment: Integrated Seurat object change name of the two conditions
Concatenating fastq.gz files across lanes
A: Concatenating fastq.gz files across lanes
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Popular Question to adeizadavid ▴ 10
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Recent Replies
Comment: Filter human transcription factors by Chris ▴ 180
Thank you so much!
Comment: Filter transcription factors by Chris ▴ 180
Yes, I do GO and GSEA to get pathway. I download the background gene at https://www.gsea-msigdb.org/gsea/msigdb/human/collections.jsp#C3 Th…
Comment: Filter transcription factors by GenoMax 134k
Thanks for the link. OP does not mention if the data is human though.
Answer: Visualize where kmers are on a reference genome by Alex Reynolds 35k
Make a bigBed file: https://www.biostars.org/p/9546293/ Then view it on the UCSC Genome Browser: http://genome.ucsc.edu/goldenPath/help/…
Comment: Integrated Seurat object change name of the two conditions by camillab. ▴ 130
great! thank you very much!
Answer: Filter transcription factors by jared.andrews07 ★ 15k
[This database](http://humantfs.ccbr.utoronto.ca/download.php) has been the best I've found.
Comment: Filter transcription factors by Ram 40k
What have you tried? Have you looked at GO annotations?
Comment: how to identify uniq genes between two gff files. by nikhil ▴ 10
yes @juke34 , I tried agat_sp_compare_two_annotations.pl for both gff files and got comparative output in table format. Thank you very muc…
Comment: Integrated Seurat object change name of the two conditions by Amitm ★ 2.2k
Yes, its similar structure. This snippet should add a new metadata column "sample.New" with what you want to do # Assuming a seurat obj. c…
Comment: Low Alignment rate by biofalconch ▴ 960
Yeap, you can sample your reads with `seqtk` like this: seqtk sample -s100 read2.fq 100 > Sample.fq Take a couple and run them throug…
Answer: obtaining circular RNAs' sequences from circBase by Barry Digby ★ 1.2k
You won't find them on circBase. circAtlas has the mature spliced sequence available. You can [search for circRNAs](https://ngdc.cncb.a…
Comment: Should I Learn Docker to Run Command Line Bioinformatics Tool? by Ram 40k
\#TIL mambaforge - better than continuum's conda images I'm guessing?
Comment: Should I Learn Docker to Run Command Line Bioinformatics Tool? by arriyaz.nstu ▴ 30
If the laptop doesn't support WSL2, then will the Docker (with linux) work?
Comment: Integrated Seurat object change name of the two conditions by camillab. ▴ 130
thanks but my metadata looks different from yours. Will it work even there are not the same "structure"? or…
Answer: Should I Learn Docker to Run Command Line Bioinformatics Tool? by ATpoint 76k
Docker is great, I use it daily since you're independent of the host computer and can share and pull the images via DockerHub. It's also gr…
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