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408 results • Page 4 of 9
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22
votes
2
replies
5.7k
views
Tutorial: Extracting genomic feature sequences from GTF/GFF files with AGAT
extract GTF GFF sequence
updated 19 months ago by ▴ 40 • written 3.0 years ago by 8.5k
6
votes
3
replies
5.7k
views
Tutorial: High Throughput Sequence Analysis With R And Bioconductor
bioconductor
updated 14 months ago by 43k • written 11.8 years ago by 100k
6
votes
11
replies
5.7k
views
6 follow
Tutorial: Add count numbers to headers in a fasta file
genome
updated 14 months ago by 43k • written 7.3 years ago by ▴ 50
20
votes
6
replies
5.6k
views
Tutorial: Open Targets and programmatic access
open-targets disease API drug
updated 13 months ago by 43k • written 7.6 years ago by ★ 5.2k
9
votes
2
replies
5.5k
views
Tutorial: From Data import to Normalization in Microarray Analysis using in R (Part I)
gene R
updated 12 months ago by 43k • written 7.8 years ago by ▴ 140
9
votes
4
replies
5.4k
views
Tutorial: Unsupervised clustering on gene expression data
gene-expression clustering RNA-seq
8 months ago by Hamid Ghaedi 3.2k
23
votes
8
replies
5.4k
views
Tutorial: A Practical (And Opinionated) Guide To Analyzing Human Methylation 450K Data
450K methylation
updated 2.3 years ago by 43k • written 9.6 years ago by 24k
0
votes
2
replies
5.4k
views
Tutorial: Install AMOS on Ubuntu 13.10
sequencing alignment software-error next-gen
updated 2.5 years ago by 43k • written 9.8 years ago by 9.7k
5
votes
3
replies
5.4k
views
Tutorial: bam2rpkm by bedtools
bam RNA-Seq bedtools rpkm
updated 13 months ago by • 0 • written 6.5 years ago by ▴ 130
12
votes
4
replies
5.3k
views
Tutorial: *FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
linux R
updated 14 months ago by 43k • written 3.2 years ago by ▴ 130
7
votes
0
replies
5.3k
views
Tutorial: Mothur Analyzing 16S Of Ngs High Through-Put Sequencing
next-gen
updated 14 months ago by 43k • written 11.9 years ago by ▴ 120
3
votes
2
replies
5.2k
views
Tutorial: Reorder Vcf Files
vcf
updated 13 months ago by 43k • written 10.9 years ago by ▴ 60
6
votes
0
replies
5.2k
views
Tutorial: How to download GEO data Quickly and easily
geo RNA-Seq R data-mining
13 months ago by Novogene ▴ 410
6
votes
10
replies
5.2k
views
Tutorial: Differentially methylated regions: Easy & Fast Identification and ANnoTation
DMR dna-methylation
updated 13 months ago by 43k • written 6.1 years ago by ▴ 370
13
votes
3
replies
5.1k
views
Tutorial: Video: Visualization of whole genome DNA methylation data in IGB
Bismark BS-Seq RNA-Seq IGB
updated 23 months ago by 43k • written 9.1 years ago by ▴ 860
12
votes
1
reply
5.0k
views
Tutorial: RepSeq data processing and analysis
immunology tcr repseq sequencing repertoire
updated 18 months ago by 43k • written 8.7 years ago by 3.5k
12
votes
6
replies
5.0k
views
Tutorial: sharing some naive codes for microarray normalization in R with whom are too new in R alike me
R
updated 21 months ago by 43k • written 8.2 years ago by ★ 4.3k
6
votes
2
replies
5.0k
views
Tutorial: Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates without alignment), mutate (create mutant genomes) and other miscellaneou…
bbmap
4 months ago by GenoMax 141k
10
votes
0
replies
4.9k
views
Tutorial: Yes .. BBMap can do that! - Part I : bbmap (aligner), bbduk (scan/trim), repair (fix PE reads) and reformat (format conversions)
bbmap
updated 13 months ago by 43k • written 3.3 years ago by 141k
50
votes
3
replies
4.8k
views
Tutorial: [[ Please read before posting a question ::: How To Ask A Good Question ]]
how-to
updated 13 months ago by 43k • written 5.3 years ago by 81k
3
votes
0
replies
4.8k
views
Tutorial: Comparing 454, Iontorrent And Miseq
454 miseq ion-torrent
updated 14 months ago by 43k • written 11.9 years ago by 100k
7
votes
0
replies
4.7k
views
Tutorial: How To Perform A Hierarchical Clustering Using Interactive Heatmaps From Gitools?
clustering
updated 13 months ago by 43k • written 10.1 years ago by ▴ 990
2
votes
0
replies
4.7k
views
Tutorial: Calculation of TSS Scores for ATAC-seq Data
next-gen-sequencing
updated 13 months ago by 43k • written 4.7 years ago by ▴ 20
16
votes
3
replies
4.6k
views
Tutorial: NCBI blast tutorial
ncbi blast
updated 12 months ago by 43k • written 8.0 years ago by 11k
15
votes
4
replies
4.6k
views
Tutorial: RNASeq tutorial for gene differential expression analysis
Transcriptomics bioconductor RNA-Seq R
updated 13 months ago by 43k • written 3.7 years ago by ▴ 340
1
vote
0
replies
4.6k
views
Tutorial: Molecular docking, estimating free energies of binding, and a tutorial for how to use AutoDock's semi-empirical force field
free-energy docking scoring
updated 2.4 years ago by 43k • written 9.7 years ago by ▴ 150
4
votes
3
replies
4.5k
views
Tutorial: How to get full taxonomy classification using taxize and myTAI
taxonomy R
updated 13 months ago by 43k • written 6.0 years ago by ★ 4.0k
6
votes
3
replies
4.5k
views
Tutorial: Principles and Workflow of 16S/18S/ITS Amplicon Sequencing
alignment sequencing RNA-seq gene
updated 13 months ago by 43k • written 5.5 years ago by ▴ 40
10
votes
3
replies
4.5k
views
Tutorial: Video: Alternative Splicing and Primer Design
RNA-Seq IGB
updated 15 months ago by 43k • written 9.6 years ago by ▴ 860
29
votes
4
replies
4.5k
views
Tutorial: Modern Statistics for Modern Biology
statistics
updated 13 months ago by 43k • written 5.2 years ago by 27k
3
votes
4
replies
4.4k
views
Tutorial: gencore: a tool to reduce sequencing noises by generating consensus reads
consensus OpenGene sequencing-noise
updated 11 months ago by 43k • written 6.0 years ago by ★ 2.5k
9
votes
0
replies
4.4k
views
Tutorial: Analysis of dbGaP data on the cloud
AWS dbGaP Cloud
updated 21 months ago by 43k • written 8.2 years ago by 19k
16
votes
3
replies
4.3k
views
Tutorial: Methylation Analysis Tutorial in R_part2
cancer methylation RNA-Seq R
updated 3.1 years ago by • 0 • written 3.5 years ago by 3.2k
9
votes
3
replies
4.2k
views
Tutorial: Ht Sequence Analysis With R And Bioconductor By The Bioinformatics Center At Uc Riverside
bioconductor
updated 14 months ago by 43k • written 11.7 years ago by 100k
5
votes
3
replies
4.2k
views
Tutorial: Chip Seq Review Papers
chip-seq
updated 13 months ago by 43k • written 11.4 years ago by ▴ 80
5
votes
1
reply
4.2k
views
Tutorial: Mini-tutorial: How to fix too-long sequence names in SyMAP
alignment
updated 16 months ago by 43k • written 8.8 years ago by 8.3k
6
votes
2
replies
4.2k
views
Tutorial: GATK method for filtering vcf lines using GT values at all or multisample level.
genome vcf genotype variant-filtration
updated 11 months ago by 43k • written 6.9 years ago by ★ 1.6k
9
votes
9
replies
4.2k
views
Tutorial: Determine % of reference genome covered by aligned SAM/BAM
reference-coverage ngs
updated 11 months ago by 43k • written 6.6 years ago by 87k
10
votes
6
replies
4.1k
views
Tutorial: CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation corlevelplot
updated 21 days ago by 43k • written 6.2 years ago by 87k
20
votes
14
replies
4.0k
views
Tutorial: Video-tutorials: How to get started using EaSeq for interactive ChIP-seq data visualization and exploration (Windows)
ChIP-Seq visualization Windows EaSeq
updated 12 months ago by 43k • written 7.9 years ago by ▴ 460
15
votes
1
reply
3.9k
views
Tutorial: Dealing with nanopore fast5 files compressed with vbz
hdf5 nanopore fast5 vbz MinKNOW
updated 19 months ago by ★ 1.8k • written 2.3 years ago by 14k
7
votes
2
replies
3.9k
views
Tutorial: How to extract fastq files from SRA data that contains both paired and unpaired reads
fastq-dump sra
updated 12 months ago by 43k • written 8.0 years ago by ▴ 850
3
votes
2
replies
3.9k
views
Tutorial: Galaxy Tutorial on ChIP-seq
galaxy ChIP-Seq
updated 11 months ago by 43k • written 7.0 years ago by ▴ 30
3
votes
1
reply
3.7k
views
Tutorial: Importance of Array Quality Control - arrayQualityMetrics (PART I)
gene R
updated 12 months ago by 43k • written 7.8 years ago by ▴ 140
1
vote
0
replies
3.7k
views
Tutorial: embarrassingly easy parallel in Python, Perl and R
parallel
updated 20 months ago by 43k • written 8.4 years ago by ▴ 70
10
votes
2
replies
3.7k
views
Tutorial: Graph visualization with igraph in R
Visualization igraph Graph R Network
updated 11 months ago by 43k • written 7.0 years ago by 27k
9
votes
14
replies
3.7k
views
6 follow
Tutorial: Install required dependencies for GATK4 on remote server without root privilege
gatk
updated 17 months ago by ▴ 10 • written 2.1 years ago by ▴ 40
0
votes
0
replies
3.6k
views
Tutorial: Park Test for Heteroskedasticity In R Commander
R Park-Test
updated 11 months ago by 43k • written 6.2 years ago by ▴ 10
3
votes
0
replies
3.6k
views
Tutorial: Video Tutorial On Conducting Whole-Exome Sequencing Research
exome-sequencing
updated 13 months ago by 43k • written 10.8 years ago by 9.7k
9
votes
0
replies
3.6k
views
Tutorial: Video: Intro to All New Features in IGB 8.2
R paired-end IGB
updated 2.1 years ago by 43k • written 9.4 years ago by ▴ 860
408 results • Page 4 of 9
Recent Votes
Answer: I'm new to cell ranger. Can single cells prepared with a protocol other than the
Answer: Piping samtools to R
Answer: How to filter columns in a raw sparse matrix in R
Convert GFF3 to splice junction BED file, for filtering variants multi-sample (RNA-seq) VCF
Answer: Convert GFF3 to splice junction BED file, for filtering variants multi-sample (
Answer: How to filter columns in a raw sparse matrix in R
Comment: Integration of transcriptomics and proteomics: difficult matching names
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Comment: Can I compare kallisto counts from samples with different amount of reads? by bioinfo ▴ 150
Thank you. I ended up using seqtk to downsample the data.
Answer: Piping samtools to R by joe ▴ 490
This is straightforward. Can perform functions on multiple lines at a time if they are loaded as such. Skeleton script below; func.1…
Comment: Where to find the homopolymer regions bed file for Hg002 genome? by Ram 43k
You should **at least** include links to the other post in each post to make users aware that you're seeking help in multiple places.
Comment: Rename multiple fastq.gz files by shenwei356 8.4k
Here's another safe solution using [brename](https://www.biostars.org/p/9487877/) ([download](https://github.com/shenwei356/brename/release…
Comment: How to filter columns in a raw sparse matrix in R by bgbs • 0
Hi, it worked, thank you so much!
Comment: Prediction tools summary - zero values by Дана • 0
Hello, Lucas. Would you be so kind to share the link or id of your Schizophrenia vcf dataset? I am a student in masters degree and I am int…
Comment: GSEA analysis in R by sansan_96 ▴ 80
One example: ``` ### ego3 <- gseGO(geneList = geneList, OrgDb = org.Hs.eg.db, ont = "CC", …
Answer: How to filter columns in a raw sparse matrix in R by bk11 ★ 2.3k
You can do this- good_cells <-c(all_good_cells_rhemac10$V1) combined_rhemac10_count_matrix_good_cells <- combined_rhemac10_count_m…
Comment: Integration of transcriptomics and proteomics: difficult matching names by ntsopoul ▴ 60
you are right! Excel just did not find it...
Answer: Integration of transcriptomics and proteomics: difficult matching names by ntsopoul ▴ 60
I found a good solution but it is really cumbersome. I use UniProt.ws to derive unique gene names (readable names) and also ambiguous name…
Comment: Merging Outputs from plink --assoc and --hardy to Produce Table by Koketso • 0
Thank you so much. How about calculating allelic odds ratios? Which plink/R command can I use for that?
Comment: Integration of transcriptomics and proteomics: difficult matching names by ATpoint 81k
For such analysis I always first translate everything to Ensembl Gene IDs (biomaRt is a good help here) and then I do the matching with thi…
Comment: Rename multiple fastq.gz files by bk11 ★ 2.3k
Of course! If it worked, accept the answer.
Comment: Integration of transcriptomics and proteomics: difficult matching names by GenoMax 141k
I can see this in the list GI:2387631 Nup42 O Gene nucleoporin 42 10.72 5 24369961 24389011 + AA867018|AB067574|AI426644|AK077066|AK07…
Comment: Rename multiple fastq.gz files by Jérémie • 0
Sorry, I misunderstood. Thank you so much for this.
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