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115 results • Page 2 of 3
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1
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2
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1.6k
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Tutorial: ViennaRNA package installation in Windows
windows rna mfold viennarna
updated 11 months ago by 43k • written 20 months ago by ▴ 20
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
1
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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
2
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0
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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
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1.4k
views
Tutorial: Data Panel In R Commander
R
updated 12 months ago by 43k • written 6.4 years ago by ▴ 10
0
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0
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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
2
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0
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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
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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
3
votes
3
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1.2k
views
Tutorial: multi-omics data integration: a case study with transcriptomics and genomics mutation data
mutation RNAseq multiomics
updated 4 months ago by ▴ 40 • written 8 months ago by ★ 3.9k
8
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2
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1.2k
views
Tutorial: Updated List of Unix tutorials 2023
Unix
updated 9 months ago by 43k • written 9 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
10 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
835
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
4
votes
0
replies
789
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
4
replies
772
views
Tutorial: Reverse pharmacology: how to predict drugs with genes or disease names?
drugs drug-targets genes
6 months ago by Coremine Medical ▴ 20
3
votes
0
replies
758
views
Tutorial: best practices for single-cell RNAseq analysis
cell single scRNAseq
11 months ago by Ming Tommy Tang ★ 3.9k
2
votes
0
replies
730
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
1
vote
0
replies
702
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
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
1
vote
0
replies
698
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
0
votes
0
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695
views
Tutorial: How to read all files into a single dataframe (merge all RNAseq count table)
RNA-seq rstats
updated 10 months ago by 43k • written 10 months ago by ★ 3.9k
0
votes
0
replies
694
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
0
votes
0
replies
667
views
Tutorial: Free Book : Computational Biology of a cell signalling pathway using R
cell-signalling R Computational-Biology
10 months ago by sinha.shriprakash ▴ 20
1
vote
5
replies
662
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
5
votes
5
replies
659
views
Tutorial: how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix RNAseq R
updated 13 days ago by • 0 • written 22 days ago by ★ 3.9k
3
votes
1
reply
657
views
Tutorial: Coordinate Systems and genomic variant description
coordinate-system HGVS normalization VCF
updated 9 months ago by 43k • written 9 months ago by 8.6k
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
2
votes
3
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643
views
Tutorial: Bulk RNA-seq: Different Expression Analysis with DEseq2
python pyDESeq2 RNA-seq
updated 4 months ago by 43k • written 4 months ago by ▴ 120
1
vote
0
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621
views
Tutorial: How to make a perfect heatmap using RNAseq data
heatmap RNAseq rstats
11 months ago by Ming Tommy Tang ★ 3.9k
7
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0
replies
612
views
Tutorial: Polygenic Risk Score Calculation
genetic-burden r prs ggplot glm
9 months ago by barslmn ★ 2.1k
2
votes
0
replies
591
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
6
votes
0
replies
580
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
1
reply
579
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
3
votes
2
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576
views
Tutorial: Single-cell RNA-seq: Preprocessing: Data integration and batch correction-2
scRNA-seq
updated 4 months ago by 82k • written 4 months ago by ▴ 120
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
0
votes
1
reply
558
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
1
vote
0
replies
552
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
0
votes
0
replies
496
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
486
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
6
votes
1
reply
484
views
Tutorial: Bulk RNA-seq: Different Expression Analysis
differential-expression RNA-seq
updated 4 months ago by 43k • written 4 months ago by ▴ 120
2
votes
1
reply
473
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
440
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
0
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0
replies
408
views
Tutorial: download metadata using GEOquery
computational-biology GEO metadata
updated 5 months ago by 43k • written 5 months ago by ★ 3.9k
0
votes
0
replies
393
views
Tutorial: Making Tile plots to show Synonymous Non-Synonymous mutation fraction
mutation ggplotify geom_tile ggplot2
5 months ago by rohitsatyam102 ▴ 860
1
vote
1
reply
374
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
0
replies
372
views
Tutorial: 4 CITE-seq tutorials
CTIE-seq
4 months ago by Ming Tommy Tang ★ 3.9k
1
vote
0
replies
369
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
0
replies
355
views
Tutorial: CITEseq tutorial
CITEseq Alevin Seurat
5 months ago by Ming Tommy Tang ★ 3.9k
0
votes
0
replies
351
views
Tutorial: Single-cell RNA-seq: Preprocessing: Preprocessing the data of scRNA-seq with omicverse-2
scRNA-seq
updated 4 months ago by 43k • written 4 months ago by ▴ 120
0
votes
0
replies
346
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
115 results • Page 2 of 3
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Forward And Reverse Strand Conventions
Answer: Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer ver
Comment: Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
Answer: Details on salmon index
ATAC-seq sample normalization
Answer: Faster Needleman-Wunsch rapid global alignment of two sequences?
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
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Comment: Add line under stat test by Nyksubuz ▴ 10
You could use [this][1] [1]: https://ggplot2.tidyverse.org/reference/geom_segment.html
Comment: API kegg - IndexError: list index out of range by Nyksubuz ▴ 10
It might be because the gene symbol is not found in the KEGG database. Add some extra error handling before parsing the results or do a man…
Comment: Sam file Header problem by saifulislam99121 • 0
Thank you for your reply. I am not very much sure about this RG. Can you explain me a bit?
Comment: GRIDSS: the Genomic Rearrangement IDentification Software Suite by dario.garvan ▴ 520
It seems that Alexandrov's [structural variant and copy number signatures][1] estimated by the [SigProfiler software ecosystem][2] aren't c…
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences? by GenoMax 142k
Then you may want to see if a program like `lastz` ([**LINK**][1]) may be useful. [1]: https://github.com/lastz/lastz
Comment: Collect dispersed executable files and run them by using bingo. by Ram 43k
What is the purpose of this tool? I have `~/bin` in my $PATH and I soft-link all executables I need to that location so why install a new t…
Comment: Merge clusters in Seurat UMAP by bk11 ★ 2.4k
Can you try this? library(dplyr) seuratobj@meta.data <- seuratobj@meta.data %>% mutate(seurat_clusters = recode(seurat_clu…
Comment: Merge clusters in Seurat UMAP by kilcdincer ▴ 10
Thank you for the response but it does not change anything.
Comment: Merge clusters in Seurat UMAP by bk11 ★ 2.4k
I have not tested but you could try something like below- seuratobj$seurat_clusters[seuratobj$seurat_clusters==5]=0 seuratobj$seur…
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences? by Gabriel R. ★ 2.9k
I know about it, isn't there a simple C++ static binary?
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences? by Gabriel R. ★ 2.9k
needle is great! but it does not handle sequences of 100k or so.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by Ram 43k
Please use the formatting bar (especially the `code` option) to present your post better. You can use backticks for inline code (\`text\` b…
Comment: Single-cell ambient RNA correction: SoupX vs decontX contamination fraction by txema.heredia ▴ 130
The point is that you need to feed the ambient algorithm a clustering list as input. This way, it checks for genes present in the soup vs g…
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i by swbarnes2 14k
Wait, so the magnitudes of the PCs are in the thousands? That's not normal for RNASeq.
Comment: Help with VG Toolkit: VCF Output is Empty by Jordan M Eizenga ▴ 460
What do you get if you use `vg stats -a` on the GAM file?
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