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114 results • Page 2 of 3
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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
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
1.5k
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
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 11 months ago by 43k • written 16 months ago by ▴ 420
2
votes
0
replies
442
views
Tutorial: Bulk RNA-seq: WGCNA (Weighted gene co-expression network analysis) analysis
WGCNA RNA-seq
updated 4 months ago by 43k • written 4 months ago by ▴ 120
2
votes
0
replies
593
views
Tutorial: Managing your data (BAM, VCF, sample, phenotype) with RDF and SPARQL.
rdf sparql data-management graph
updated 8 months ago by 43k • written 8 months ago by 161k
2
votes
0
replies
487
views
Tutorial: Understanding Hierarchical Clustering in R, Distance Measures, and Linkage Methods
clustering gene-expression rstats
updated 10 months ago by 43k • written 10 months ago by ★ 3.9k
2
votes
0
replies
731
views
Tutorial: Get a list of genes associated with a drug in 1 min
drug genes drug-targets
updated 11 months ago by 43k • written 11 months ago by ▴ 20
2
votes
1
reply
474
views
Tutorial: Single-cell RNA-seq: Preprocessing: Clustering space and evaluation
scRNA-seq space clustering
updated 4 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
233
views
Tutorial: Premade library preparation – considerations, tips and tricks (II)
Illumina. Premade-library. NovaSeqX.
11 weeks ago by Novogene ▴ 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 6 months ago by • 0 • written 15 months ago by ★ 1.6k
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 10 months ago by 43k • written 10 months ago by ★ 3.9k
1
vote
0
replies
371
views
Tutorial: Single-cell RNA-seq: Preprocessing: Data integration and batch correction
scRNA-seq
updated 4 months ago by 43k • written 4 months ago by ▴ 120
1
vote
1
reply
376
views
Tutorial: Bulk RNA-seq: Protein-Protein interaction (PPI) analysis by String-db
STRING ppi
updated 4 months ago by 43k • written 4 months ago by ▴ 120
1
vote
2
replies
1.6k
views
Tutorial: ViennaRNA package installation in Windows
windows rna mfold viennarna
updated 11 months ago by 43k • written 20 months ago by ▴ 20
1
vote
0
replies
307
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA
scRNA-seq SCSA
updated 4 months ago by 43k • written 4 months ago by ▴ 120
1
vote
5
replies
664
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype annotation migration(mapping) with TOSICA
scRNA-seq TOSICA
updated 3 months ago by 43k • written 4 months ago by ▴ 120
1
vote
0
replies
703
views
Tutorial: How to convert gene ids in R
computational-biology gene-id rstats
updated 10 months ago by 43k • written 10 months ago by ★ 3.9k
1
vote
0
replies
220
views
Tutorial: DNA Methylation: Sequencing Techniques
WGBS RRBS
29 days ago by Novogene ▴ 420
1
vote
0
replies
700
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
356
views
Tutorial: CITEseq tutorial
CITEseq Alevin Seurat
5 months ago by Ming Tommy Tang ★ 3.9k
1
vote
2
replies
901
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
621
views
Tutorial: How to make a perfect heatmap using RNAseq data
heatmap RNAseq rstats
11 months ago by Ming Tommy Tang ★ 3.9k
1
vote
0
replies
649
views
Tutorial: common mistakes in using spreadsheets
excel spreadsheet structured-data
updated 9 months ago by 43k • written 9 months ago by ★ 3.9k
1
vote
4
replies
3.4k
views
Tutorial: Applying machine learning to NGS transcriptomic data
next-gen RNA-Seq
updated 12 months ago by 43k • written 6.0 years ago by ▴ 340
1
vote
0
replies
553
views
Tutorial: How to convert raw counts to TPM for TCGA data and make a heatmap across cancer types
RNAseq heatmap rstats TCGA
6 months ago by Ming Tommy Tang ★ 3.9k
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 11 months ago by 43k • written 16 months ago by ▴ 420
1
vote
0
replies
1.5k
views
Tutorial: Fall 2017 Introduction to Human Genomics for Clinical Informaticists
genome
updated 12 months ago by 43k • written 6.4 years ago by ▴ 90
1
vote
0
replies
559
views
Tutorial: cellular niches analysis with spatial transcriptome data in Seurat and Bioconductor
transcriptome rstats spatial single-cell
9 months ago by Ming Tommy Tang ★ 3.9k
1
vote
0
replies
293
views
Tutorial: Bulk RNA-seq: TCGA database preprocess
RNA-seq
updated 4 months ago by 43k • written 4 months ago by ▴ 120
1
vote
0
replies
373
views
Tutorial: 4 CITE-seq tutorials
CTIE-seq
4 months ago by Ming Tommy Tang ★ 3.9k
1
vote
0
replies
837
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
1
vote
0
replies
308
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
0
votes
0
replies
1.6k
views
Tutorial: PLS SEM (Partial Least Square Sructural Equation Modeling) Analysis WarpPLS 6
R
updated 12 months ago by 43k • written 6.3 years ago by ▴ 10
0
votes
1
reply
559
views
Tutorial: TAPIS installation and usage
APA Iso-seq splicing TAPIS analysis alternative
updated 8 months ago by 82k • written 8 months ago by ▴ 30
0
votes
0
replies
305
views
Tutorial: Single-cell RNA-seq: Preprocessing: Data integration and batch correction-3
scRNA-seq
updated 4 months ago by 43k • written 4 months ago by ▴ 120
0
votes
0
replies
497
views
Tutorial: Using easyPubMed and scholar package to get all citations of your paper
scholar easyPubMed
6 months ago by rohitsatyam102 ▴ 860
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
0
votes
1
reply
1.9k
views
Tutorial: Nonparametric Regression STATA 15
STATA-15 Nonparametric-Regression STATA
updated 12 months ago by 43k • written 6.4 years ago by ▴ 10
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
0
votes
0
replies
347
views
Tutorial: How to convert sra files to fastq files using parallelized fastq-dump
fastq sra
3 months ago by Ming Tommy Tang ★ 3.9k
0
votes
1
reply
580
views
Tutorial: Single-cell RNA-seq: Preprocessing: Preprocessing the data of scRNA-seq with omicverse-1
scRNA-seq
updated 4 months ago by 43k • written 4 months ago by ▴ 120
0
votes
0
replies
268
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA-3
scRNA-seq SCSA
updated 4 months ago by 43k • written 4 months ago by ▴ 120
0
votes
1
reply
313
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with MetaTiME
scRNA-seq MetaTiME
updated 4 months ago by 43k • written 4 months ago by ▴ 120
0
votes
0
replies
287
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA-2
scRNA-seq SCSA
updated 4 months ago by 43k • written 4 months ago by ▴ 120
0
votes
0
replies
2.9k
views
Tutorial: Autocorrelation With Breusch Godfrey Serial Correlation LM Test R Commander
LM-Test R Autocorrelation Breusch-Godfrey
updated 12 months ago by 43k • written 6.4 years ago by ▴ 10
0
votes
0
replies
699
views
Tutorial: How to start disease research quickly and easily?
proteins pathways disease research-design genes
11 months ago by Coremine Medical ▴ 20
0
votes
0
replies
273
views
Tutorial: How to Label the Y Axis with percentage sign and Order Bars in ggplot2 using a single cell dataset
seurat single-cell ggplot2
4 months ago by Ming Tommy Tang ★ 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
114 results • Page 2 of 3
Recent Votes
Comment: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: Details on salmon index
Answer: Generating consensus sequence from bam file
Answer: Short Read Data Genome Assembly
Comment: API kegg - IndexError: list index out of range
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Recent Replies
Comment: In one PCA plot, can I calculate the percentage of different factors that contri by marco.barr ▴ 130
great team work! why can't you access and do the calculation for the other components too? can't you extract the information from the other…
Comment: zero TPM for many gene including housekeeping when using kallisto by ATpoint 82k
Yes, but this is what I am saying: GAPDH in human has at least 6 annotated transcripts. Have you looked at all of them? Maybe that particul…
Comment: zero TPM for many gene including housekeeping when using kallisto by ashkan ▴ 160
@atpoint these are from PBMC. no they are different genes. for example ENST00000229239.10 is GAPDH. in STAR I got a lot of reads aligned …
Comment: zero TPM for many gene including housekeeping when using kallisto by ashkan ▴ 160
@dariober: I have to use kallisto for our downstream pipeline.
Comment: zero TPM for many gene including housekeeping when using kallisto by ATpoint 82k
Which celltype is this? Are these transcripts of the same gene, and of which gene?
Comment: zero TPM for many gene including housekeeping when using kallisto by ashkan ▴ 160
@atpoint the question is updated. the first command shows how the index is built.
Comment: Help! Reconstruction of locus, order contigs by dthorbur ★ 2.0k
Is the *de novo* annotation required for each contig? Reconstructing homologous regions in many genomes can be tricky regardless, but is es…
Comment: In one PCA plot, can I calculate the percentage of different factors that contri by diqixiaoyaoer ▴ 20
You can have a look on my answer. I have post it below.
Answer: In one PCA plot, can I calculate the percentage of different factors that contri by diqixiaoyaoer ▴ 20
Here is my script that can be used to calculate how much degree that different factors contribute to PCA variance (PC1 and PC2). # …
Comment: Details on salmon index by Lorenzo • 0
Thank you so much for the beautiful explanation. Just one more curiosity. So in the first versions Salmon utilized RapMap to index and then…
Comment: What marks a De-Novo Genome assembly as FAILED? by dthorbur ★ 2.0k
I'm a little confused about your experimental design. Are you making 45 different assemblies? Or are all the samples from the same individu…
Comment: zero TPM for many gene including housekeeping when using kallisto by ATpoint 82k
You should be stating how you constructed the index, and include the actual lines for the problematic genes from the abundance files. Note …
Comment: zero TPM for many gene including housekeeping when using kallisto by dariober 14k
You could try [salmon](https://combine-lab.github.io/salmon/getting_started/) to see if the problem is with kallisto or with the pseudo-ali…
Comment: solution-Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* err by GenoMax 142k
> INPUT FILE error: could not open input file /geneInfo.tab Based on the error it appears that the input file you are providing could not …
Answer: How to handle duplicated genes in TCGA data? by txema.heredia ▴ 130
Having duplicate gene symbols is pretty common. Why do you need to work with gene symbols? To compare them to external datasets? Or just fo…
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