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99
votes
16
replies
32k
views
18 follow
Tutorial: Heatmaps in R
heatmap R
updated 8 months ago by 41k • written 7.3 years ago by 26k
21
votes
2
replies
5.2k
views
Tutorial: Extracting genomic feature sequences from GTF/GFF files with AGAT
extract GTF GFF sequence
updated 15 months ago by ▴ 40 • written 2.6 years ago by 8.4k
31
votes
6
replies
11k
views
Tutorial: A simple tutorial for a complex ComplexHeatmap
clustering pam arthritis ComplexHeatmap
updated 8 months ago by 41k • written 3.6 years ago by 86k
8
votes
0
replies
2.5k
views
Tutorial: Pipes in R: An introduction and some advanced tips and tricks.
R
2.7 years ago by rpolicastro 12k
238
votes
176
replies
90k
views
73 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq Survival TCGA
updated 6 months ago by 41k • written 8.4 years ago by ★ 4.7k
6
votes
0
replies
2.1k
views
Tutorial: data.frames in R: How vectorization can save you time and heartache
R
2.7 years ago by rpolicastro 12k
8
votes
1
reply
1.3k
views
Tutorial: Split a 'linearised' (flattened) FASTA sequence into multi-line using AWK
fasta awk
updated 8 months ago by 41k • written 2.7 years ago by 86k
21
votes
10
replies
6.3k
views
Tutorial: Finding the significance of the overlap between 2 or more gene sets using simulation in R.
tidyverse gene R
updated 8 months ago by 41k • written 3.3 years ago by 12k
12
votes
2
replies
1.2k
views
Tutorial: Factors in R - How do they work, and how did I break my data?
R
updated 8 months ago by 41k • written 2.7 years ago by 12k
149
votes
35
replies
61k
views
33 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics next-gen
updated 9 months ago by 41k • written 11.0 years ago by ★ 1.6k
15
votes
2
replies
3.6k
views
Tutorial: Methylation Analysis Tutorial in R_part2
cancer methylation RNA-Seq R
updated 8 months ago by 41k • written 3.2 years ago by 3.1k
16
votes
7
replies
15k
views
Tutorial: Integrating VDJ sequencing data with Seurat
VDJ Seurat sc-RNAseq clonotyping
updated 8 months ago by 41k • written 4.5 years ago by ▴ 310
290
votes
33
replies
102k
views
25 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 9 months ago by 41k • written 10.1 years ago by 20k
5
votes
2
replies
4.4k
views
Tutorial: Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates without alignment), mutate (create mutant genomes) and other miscellaneou…
bbmap
7 days ago by GenoMax 136k
11
votes
0
replies
6.1k
views
Tutorial: Yes .. BBMap can do that! - Part II randomreads (read simulation), demuxbyname/filterbyname, bbsplit (read binning/decontamination) and pileup (cover…
bbmap
updated 8 months ago by 41k • written 2.9 years ago by 136k
10
votes
0
replies
4.2k
views
Tutorial: Yes .. BBMap can do that! - Part I : bbmap (aligner), bbduk (scan/trim), repair (fix PE reads) and reformat (format conversions)
bbmap
updated 8 months ago by 41k • written 2.9 years ago by 136k
11
votes
1
reply
2.5k
views
Tutorial: Guidelines for the computational analysis of single-cell RNA sequencing data
scRNA-seq
updated 8 months ago by 41k • written 2.9 years ago by ★ 25k
40
votes
9
replies
11k
views
10 follow
Tutorial: Resources for flow cytometry bioinformatics
single-cell flow-cytometry
updated 9 months ago by 41k • written 9.7 years ago by ★ 1.9k
0
votes
1
reply
2.8k
views
Tutorial: Getting the lineage of an organism from NCBI taxonomy data
biosql python taxonomy
updated 8 months ago by 41k • written 5.3 years ago by ▴ 320
76
votes
13
replies
15k
views
12 follow
Tutorial: Exploring cancer mutation data portals
TCGA Cancer ICGC Data-Portal Mutation
updated 2.2 years ago by 41k • written 9.5 years ago by 19k
6
votes
10
replies
5.0k
views
Tutorial: Differentially methylated regions: Easy & Fast Identification and ANnoTation
DMR dna-methylation
updated 8 months ago by 41k • written 5.8 years ago by ▴ 370
43
votes
6
replies
12k
views
Tutorial: Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
ensembl maf tcga vcf
updated 9 months ago by 41k • written 9.9 years ago by 6.0k
5
votes
3
replies
5.1k
views
Tutorial: bam2rpkm by bedtools
bam RNA-Seq bedtools rpkm
updated 8 months ago by • 0 • written 6.1 years ago by ▴ 130
16
votes
11
replies
7.9k
views
Tutorial: How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking
meta how-to documentation
8 months ago by Ram 41k
104
votes
6
replies
25k
views
6 follow
Tutorial: Creating workflows with snakemake and conda
workflow snakemake conda
updated 8 months ago by 41k • written 5.3 years ago by 16k
18
votes
40
replies
17k
views
16 follow
Tutorial: Easy way to run easily orthoMCL (Copy & paste)
all-v-all orthomcl
updated 3.4 years ago by • 0 • written 7.4 years ago by ▴ 170
24
votes
4
replies
7.2k
views
Tutorial: Using EnrichedHeatmap for visualization of NGS experiments
heatmap chip-seq atac-seq EnrichedHeatmap
updated 8 months ago by 41k • written 4.3 years ago by 78k
15
votes
4
replies
4.4k
views
Tutorial: RNASeq tutorial for gene differential expression analysis
Transcriptomics bioconductor RNA-Seq R
updated 8 months ago by 41k • written 3.4 years ago by ▴ 340
26
votes
0
replies
2.3k
views
Tutorial: Resources / databases for clinical interpretation of cancer variants
interpretation cancer annotation variant
updated 8 months ago by 41k • written 4.2 years ago by 19k
10
votes
1
reply
2.2k
views
Tutorial: introduce a tool for fast identification of SARS-CoV-2 and other microbes from sequencing data
SARS-CoV-2 fastv COVID-19
updated 8 months ago by 41k • written 3.7 years ago by ★ 2.5k
60
votes
52
replies
42k
views
23 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
plotly R volcano-plot
updated 8 months ago by 41k • written 7.2 years ago by ★ 3.4k
13
votes
7
replies
5.6k
views
Tutorial: STARsolo config for 10x Chromium v1, v2, v3
Chromium 10x STARsolo STAR
updated 8 months ago by 41k • written 3.2 years ago by 86k
18
votes
22
replies
8.5k
views
10 follow
Tutorial: Create de novo repeat library
de-novo repeat annotation
updated 11 weeks ago by ▴ 20 • written 4.0 years ago by 8.4k
0
votes
0
replies
1.0k
views
Tutorial: BrainArray CDF, annotation, etc
db brainarray cdf
updated 8 months ago by 41k • written 3.2 years ago by 86k
12
votes
0
replies
2.5k
views
Tutorial: Long versus wide data for plotting genomics data in R.
ggplot2 tidyverse data.table R
updated 8 months ago by 41k • written 3.3 years ago by 12k
76
votes
70
replies
18k
views
18 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
updated 8 months ago by 41k • written 5.8 years ago by 86k
1
vote
1
reply
1.3k
views
Tutorial: Downloading GnuWin and using to convert txt to bed file for windows users
bed bed2txt sequencing txt
updated 8 months ago by 41k • written 3.3 years ago by • 0
4
votes
3
replies
4.4k
views
Tutorial: How to get full taxonomy classification using taxize and myTAI
taxonomy R
updated 8 months ago by 41k • written 5.7 years ago by ★ 3.9k
4
votes
1
reply
1.3k
views
Tutorial: Real World BEDtools. Practical Examples for Variant Filtering and Gene Annotations
BED BEDtools
updated 8 months ago by 41k • written 3.3 years ago by ▴ 40
3
votes
0
replies
3.4k
views
Tutorial: Sorting GFF/GTF files
gtf gff
updated 9 months ago by 41k • written 3.4 years ago by 8.4k
20
votes
6
replies
5.3k
views
Tutorial: Open Targets and programmatic access
open-targets disease API drug
updated 8 months ago by 41k • written 7.2 years ago by ★ 5.2k
2
votes
2
replies
1.9k
views
Tutorial: Human mitochondrial DNA annotation in SnpEff
chrMT SNP snpEff
updated 8 months ago by 41k • written 3.4 years ago by 3.2k
12
votes
5
replies
2.2k
views
Tutorial: FASTA file split
fasta
updated 8 months ago by 41k • written 3.5 years ago by 8.4k
0
votes
0
replies
1.6k
views
Tutorial: VIDEO: Installing BLAST Databases on Your Own Computer
BLAST-databases Linux sequence MacOSX
updated 8 months ago by 41k • written 3.5 years ago by ▴ 450
0
votes
0
replies
940
views
Tutorial: VIDEO: BLAST Searches Through a Data Science Lens
Covid19 Data-Science sequence BLAST
updated 8 months ago by 41k • written 3.5 years ago by ▴ 450
2
votes
1
reply
1.5k
views
Tutorial: A very simple way to detect viruses and microorganisms from mNGS FASTQ data using fastv
SARS-CoV-2 fastv COVID-19 viruses
updated 8 months ago by 41k • written 3.5 years ago by ★ 2.5k
72
votes
27
replies
27k
views
16 follow
Tutorial: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 5 days ago by • 0 • written 9.8 years ago by 99k
59
votes
43
replies
20k
views
18 follow
Tutorial: Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
pbalign pacbio arrow smrt-limk
updated 8 months ago by 41k • written 6.2 years ago by ★ 1.4k
20
votes
7
replies
6.1k
views
Tutorial: Showing up and down regulated GO and pathway using enrichR and ggplot2
ggplot2 RNA-Seq R
updated 8 months ago by 41k • written 5.2 years ago by ▴ 770
4
votes
0
replies
1.7k
views
Tutorial: NIH CDE browser for TCGA clinical data CDE codes
nih tcga metadata cde
updated 8 months ago by 41k • written 3.7 years ago by 86k
384 results • Page 3 of 8
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A: next generation of BLAST2GO: software recommendations needed
Answer: Where can I get a list of SNPs mapping overlapping genes in humans?
Answer: Where can I get a list of SNPs mapping overlapping genes in humans?
Where to download excel file to include major human disease, prevalence and incidence?
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Recent Replies
Comment: Alternative to Gentrome? by GenoMax 136k
Curious as to what is `gentrome`? Genome decoy + transcriptome?
Comment: Java class error message when using BBDuk by GenoMax 136k
> I have cloned the bbmap Git Hub You are not using official repository then. BBMap is available from [**SourceForge**][1] or Bitbucket…
Comment: identifying SNPs from short read sequencing data by GenoMax 136k
Short answer is yes. Are you planning to sequence the entire genome after mutagenesis or only the selected region? In any case the analysis…
Comment: using RSEM with non Trinity assembly by jen • 0
Thanks! I'll try it out.
Comment: How to run Aracne cytoscape plugin ? by gentlemonster • 0
@prithvi.mastermind have you been able to find a solution to this? if so, could you share how you did it?
Comment: Read count vs Depth by Brian Bushnell 20k
Yes, that is correct.
Comment: Dimensionality reduction on data sets with variable dimensions by Mensur Dlakic ★ 25k
You can try DNA/RNA language models and extract their embeddings based on your sequences. Those should be of the same length and presumably…
Comment: Dimensionality reduction on data sets with variable dimensions by rtrende ▴ 80
I see what you mean that this method isn’t a perfect way to compare segments but I’ve had a very hard time finding other similarity metrics…
Comment: How should I run ssgsea analysis ? by sure ▴ 100
@Ram there are 2 post from me that are that way...stupidity of mine this one and "p-value combination methods" can you remove those comment…
Answer: autodock vina on mac by Ram 41k
I googled "autodock vina virtualbox" and the 2nd web link I see is to this page: https://bioinformaticsreview.com/20220117/tutorial-how-to-…
Answer: How can I obtain the DNA sequences of each CDS for several genbank files? by Ram 41k
This is a simple python issue. You're missing indentation after your first `if`: ```py cds = [] for feature in genome.features: i…
Comment: CIGAR and query sequence lengths differ by ManuelDB ▴ 80
ok I have added a function that checks CIGAR and query sequence lengths and if disagreement is detected, stop the analysis. In that read so…
Comment: Rstudio cloud by synat.keam ▴ 80
Hi Ram, thanks, I am using one that is from Sever which I can specify cpu core and RAM etc. thanks you
Comment: LCA from BLAST output by Negin • 0
Does anyone know an R function/code to do the LCA from a blast output that already contains all the ranks on each column? Something like th…
Comment: CIGAR and query sequence lengths differ by ManuelDB ▴ 80
Hi Istvan Albert. I have seen your answer. Many thanks Regarding the mock question. I have found a solution to that problem. I will put th…
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