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128 results • Page 3 of 3
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0
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368
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Tutorial: 4 CITE-seq tutorials
CTIE-seq
4 months ago by Ming Tommy Tang ★ 3.9k
0
votes
0
replies
263
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA-3
scRNA-seq SCSA
updated 3 months ago by 43k • written 4 months ago by ▴ 120
1
vote
0
replies
832
views
Tutorial: List of Machine Learning-Based Scoring Function Papers
machine-learning docking papers
updated 6 months ago by 43k • written 14 months ago by ▴ 10
0
votes
0
replies
3.6k
views
Tutorial: SFA (Stochastic Frontier Analysis) STATA 14
R
updated 12 months ago by 43k • written 6.3 years ago by ▴ 10
3
votes
0
replies
753
views
Tutorial: best practices for single-cell RNAseq analysis
cell single scRNAseq
10 months ago by Ming Tommy Tang ★ 3.9k
5
votes
0
replies
1.7k
views
Tutorial: GEO data mining (IB) - Downloading Sequence Read Archive (SRA) raw data
geo RNA-Seq data-mining SRA
updated 11 months ago by 43k • written 16 months ago by ▴ 420
3
votes
0
replies
2.2k
views
Tutorial: Deep Learning for Cancer Immunotherapy
keras tensorflow
updated 12 months ago by 43k • written 6.3 years ago by 22k
1
vote
0
replies
618
views
Tutorial: How to make a perfect heatmap using RNAseq data
heatmap RNAseq rstats
10 months ago by Ming Tommy Tang ★ 3.9k
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 5.8 years ago by • 0
6
votes
0
replies
575
views
Tutorial: 12 useful command line tools and tricks for genomics data science
unix
updated 3 months ago by 11k • written 3 months ago by ★ 3.9k
0
votes
0
replies
2.2k
views
Tutorial: Transforming (Transformation) Data LN, Log, SQRT In R Commander
R
updated 12 months ago by 43k • written 6.3 years ago by ▴ 10
1
vote
0
replies
304
views
Tutorial: How to Use Biomart to Find Mouse Orthologs for Human Genes
ids gene bioconductor
4 months ago by Ming Tommy Tang ★ 3.9k
4
votes
0
replies
787
views
Tutorial: How to do GSEA in R for RNAseq data
gsea RNAseq rstats
10 months ago by Ming Tommy Tang ★ 3.9k
0
votes
0
replies
3.1k
views
Tutorial: Normality Test For JB (Jarque Bera) Test R Commander
Jarque-Bera-Test R-Commander
updated 12 months ago by 43k • written 6.4 years ago by ▴ 10
2
votes
0
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1.5k
views
Tutorial: Webinar: Extracting research evidence from publications
text-mining ontology pubmed
updated 12 months ago by 43k • written 6.2 years ago by ▴ 60
1
vote
0
replies
303
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA
scRNA-seq SCSA
updated 3 months ago by 43k • written 4 months ago by ▴ 120
0
votes
0
replies
694
views
Tutorial: How to start disease research quickly and easily?
proteins pathways disease research-design genes
11 months ago by Coremine Medical ▴ 20
2
votes
0
replies
436
views
Tutorial: Bulk RNA-seq: WGCNA (Weighted gene co-expression network analysis) analysis
WGCNA RNA-seq
updated 3 months ago by 43k • written 4 months ago by ▴ 120
2
votes
0
replies
6.9k
views
Tutorial: How to - Install Python packages in a virtual environment (virtualenv)
ubuntu cutadapt virtualenv python windows
updated 12 months ago by 43k • written 6.4 years ago by ▴ 320
2
votes
0
replies
3.3k
views
Tutorial: use the tool slicer to split big files (like FASTQ) to smaller files for parallel processing
opengene slicer fastq splitter
updated 11 months ago by 43k • written 6.6 years ago by ★ 2.5k
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 5.9 years ago by ▴ 340
0
votes
0
replies
251
views
Tutorial: Parsing HMMER output
HMMER
updated 7 weeks ago by 142k • written 7 weeks ago by ▴ 140
2
votes
0
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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 10 months ago by 43k • written 10 months ago by ★ 3.9k
0
votes
0
replies
490
views
Tutorial: Using easyPubMed and scholar package to get all citations of your paper
scholar easyPubMed
6 months ago by rohitsatyam102 ▴ 860
2
votes
0
replies
2.1k
views
Tutorial: How to display Agilent CGH array in IGV
IGV CGH
updated 12 months ago by 43k • written 6.4 years ago by ★ 2.4k
1
vote
0
replies
646
views
Tutorial: common mistakes in using spreadsheets
excel spreadsheet structured-data
updated 9 months ago by 43k • written 9 months ago by ★ 3.9k
0
votes
0
replies
1.4k
views
Tutorial: Data Panel In R Commander
R
updated 12 months ago by 43k • written 6.4 years ago by ▴ 10
5
votes
0
replies
2.2k
views
Tutorial: Installing multiprocessor-capable MEME to work with a Slurm job scheduler environment
slurm meme parallel
updated 12 months ago by 43k • written 6.7 years ago by 35k
128 results • Page 3 of 3
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Answer: Difference between Genotype 0|1 and 1|0 in VCF file?
Answer: how to keep reads in a fasta file based on a seq id list in R?
Answer: The total expressed genes in RNA-Seq data
C: Re-arrange conditions in Seurat
Genome Visualization Tools
Answer: Genome Visualization Tools
Answer: RSeQC : infer_experiment.py Error: Could not retrieve index file
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Recent Replies
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred by Juke34 8.6k
Right I heard there is an issue since Perl v5.36. You may have better luck using conda. Or the best way is to use the container. Or downgra…
Answer: Alphaphold 3 pLDDT coloring scheme in chimerax? by Mensur Dlakic ★ 27k
pLDDT scores are stored in the so-called B-factor column in PDB files. Below the `File` ribbon select `Molecule Display` and click on `b-fa…
Comment: Genome Visualization Tools by dlera.lozano ▴ 10
Thank you so much
Answer: Doubt about the process of annotation, detection, identification and classificat by Mensur Dlakic ★ 27k
Depends on the context. `TE detection` and `TE identification` could mean the same thing if they refer to presence/absence of TEs. `TE iden…
Comment: featureCounts output summary assigned value higher than uniquely mapped reads fr by Ram 43k
Please accept your own answer to mark the post as solved.
Comment: RSeQC : infer_experiment.py Error: Could not retrieve index file by Ram 43k
A small educational note: if an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accep…
Comment: RSeQC : infer_experiment.py Error: Could not retrieve index file by Prawesh • 0
thanks, it's working now.
Answer: Genome Visualization Tools by GenoMax 142k
@cmdcolin has a great list here: https://github.com/cmdcolin/awesome-genome-visualization
Answer: RSeQC : infer_experiment.py Error: Could not retrieve index file by Trivas ★ 1.8k
You need to have indexed your bam/sam file using `samtools index`
Answer: Using ggplotly in R by jared.andrews07 ★ 16k
The simple answer is to plot it natively with plotly rather than use `ggplotly`. See [this stackoverflow answer](https://stackoverflow.com/…
Comment: Why does assigning genes with biomart give me different values than using a tran by GenoMax 142k
According to HUGO there is only one [**ZSCAN2 gene**][1] and it points to the first Ensembl gene ID (ENSG00000176371). Ensembl is annotatin…
Answer: RNAseq RNA content by noodle ▴ 580
There are many tools for this. I recommend [gatk (picard) CollectRnaSeqMetrics][1] or alternatively [RSeQC][2] and then run [multiqc][3…
Comment: Where to get the following bed file? by wyuan37 • 0
Hi, I emailed them and did get the bed file! Thank you so much.
Comment: Where to get the following bed file? by wyuan37 • 0
Thanks! Super helpful.
Answer: Post-imputation QC for input into GWAS analyses by LauferVA 4.2k
1. Imputation algorithms will output log files indicating, among other things, accuracy of imputation. We can't comment on specifics as we …
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