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325 results • Page 3 of 7
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5
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Tutorial: Using The Biomart Perl Api For Simple Queries
api perl biomart
updated 7 months ago by 40k • written 11.0 years ago by 20k
9
votes
5
replies
2.1k
views
Tutorial: What is new in samtools release 1.5 [Solstice Release] (21st June 2017)
samtools
updated 4 months ago by 40k • written 6.2 years ago by 98k
15
votes
5
replies
12k
views
6 follow
Tutorial: Easy way to do GO enrichment in R
enrichr RNA-Seq gene R
updated 6 months ago by 40k • written 5.8 years ago by ▴ 760
64
votes
5
replies
7.0k
views
10 follow
Tutorial: Informatics of RNA-Seq.
next-gen RNA-Seq
updated 11 months ago by 40k • written 8.1 years ago by 12k
5
votes
5
replies
6.5k
views
Tutorial: use firehose_get to download TCGA data
tcga RNA-Seq
updated 4 months ago by 40k • written 5.9 years ago by ▴ 130
10
votes
5
replies
21k
views
Tutorial: Y-DNA and mtDNA Haplogroup Predictor
haplogroup
updated 6 months ago by 40k • written 5.2 years ago by ★ 9.3k
19
votes
4
replies
8.6k
views
Tutorial: Rna Seq Experimental Design For Measuring Differential Gene Expression
RNA-seq
updated 7 months ago by 40k • written 10.6 years ago by 98k
1
vote
4
replies
3.1k
views
Tutorial: Applying machine learning to NGS transcriptomic data
next-gen RNA-Seq
updated 4 months ago by 40k • written 5.4 years ago by ▴ 340
3
votes
4
replies
4.2k
views
Tutorial: gencore: a tool to reduce sequencing noises by generating consensus reads
consensus OpenGene sequencing-noise
updated 4 months ago by 40k • written 5.4 years ago by ★ 2.4k
1
vote
4
replies
3.1k
views
Tutorial: How to install C++ compilers/make from GNU for Gromacs?
Gromacs Cpp-compilers GNU
updated 5 months ago by 40k • written 7.3 years ago by ▴ 10
3
votes
4
replies
3.5k
views
Tutorial: Gene Set Enrichment Analysis on T-BioInfo
gene RNA-Seq
updated 4 months ago by 40k • written 4.9 years ago by ▴ 340
9
votes
4
replies
4.0k
views
Tutorial: Unsupervised clustering on gene expression data
gene-expression clustering RNA-seq
6 weeks ago by Hamid Ghaedi 3.0k
32
votes
4
replies
7.0k
views
Tutorial: Fast LD computation from VCF files using tomahawk
ld snp vcf vcftools bcftools
updated 6 months ago by 40k • written 4.9 years ago by ★ 1.6k
6
votes
4
replies
7.2k
views
Tutorial: Overlay Multiple Tracks In Ucsc Browser [Quick Minimal Tutorial]
visualization ChIP-seq RNA-seq ucsc-genome-browser bigwig
updated 7 months ago by 40k • written 10.5 years ago by 11k
15
votes
4
replies
4.3k
views
Tutorial: RNASeq tutorial for gene differential expression analysis
Transcriptomics bioconductor RNA-Seq R
updated 6 months ago by 40k • written 3.2 years ago by ▴ 330
20
votes
4
replies
14k
views
Tutorial: How To Install A Specific Cdf Package For Use In Bioconductor
bioconductor affymetrix
updated 7 months ago by 40k • written 10.5 years ago by 20k
12
votes
4
replies
2.0k
views
Tutorial: Tutorials for Library Normalization in DESeq2 and EdgeR
EdgeR DESeq2
updated 6 months ago by 40k • written 6.0 years ago by ▴ 590
10
votes
4
replies
3.2k
views
Tutorial: CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation corlevelplot
updated 4 months ago by 40k • written 5.6 years ago by 86k
24
votes
4
replies
6.9k
views
Tutorial: Using EnrichedHeatmap for visualization of NGS experiments
heatmap chip-seq atac-seq EnrichedHeatmap
updated 6 months ago by 40k • written 4.1 years ago by 76k
12
votes
4
replies
5.0k
views
Tutorial: *FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
linux R
updated 7 months ago by 40k • written 2.6 years ago by ▴ 130
20
votes
4
replies
8.4k
views
Tutorial: DE analysis by edgeR
RNA-Seq R edgeR
updated 5 months ago by 40k • written 7.0 years ago by ★ 4.2k
28
votes
4
replies
4.1k
views
Tutorial: Modern Statistics for Modern Biology
statistics
updated 6 months ago by 40k • written 4.7 years ago by 26k
20
votes
4
replies
2.4k
views
Tutorial: Bash One-liners collection on Github
bash linux shell
updated 6 months ago by 40k • written 4.4 years ago by ▴ 180
10
votes
4
replies
10k
views
Tutorial: Using the MinION MinKNOW software on Ubuntu 1604
long-reads oxford-nanopore minion
updated 6 months ago by 40k • written 4.2 years ago by 5.5k
50
votes
3
replies
4.4k
views
Tutorial: [[ Please read before posting a question ::: How To Ask A Good Question ]]
how-to
updated 6 months ago by 40k • written 4.7 years ago by 76k
1
vote
3
replies
3.0k
views
Tutorial: resolving error of sspace_standard
software-error Assembly
updated 5 months ago by 40k • written 7.1 years ago by ▴ 300
9
votes
3
replies
4.0k
views
Tutorial: Ht Sequence Analysis With R And Bioconductor By The Bioinformatics Center At Uc Riverside
bioconductor
updated 7 months ago by 40k • written 11.1 years ago by 98k
44
votes
3
replies
12k
views
Tutorial: A Wet-Lab Guide to 'what I wish I had known' for Computational Biology
bioinformatics computational-biology
updated 5 months ago by 40k • written 7.5 years ago by ★ 3.2k
51
votes
3
replies
22k
views
Tutorial: Sam File Format - Lesser Known Tips And Tricks
sam
updated 7 months ago by 40k • written 10.7 years ago by ▴ 300
6
votes
3
replies
5.5k
views
Tutorial: High Throughput Sequence Analysis With R And Bioconductor
bioconductor
updated 7 months ago by 40k • written 11.2 years ago by 98k
10
votes
3
replies
4.3k
views
Tutorial: Video: Alternative Splicing and Primer Design
RNA-Seq IGB
updated 8 months ago by 40k • written 9.0 years ago by ▴ 860
5
votes
3
replies
5.0k
views
Tutorial: bam2rpkm by bedtools
bam RNA-Seq bedtools rpkm
updated 6 months ago by • 0 • written 5.9 years ago by ▴ 130
1
vote
3
replies
688
views
Tutorial: Gibbs Sampling Algorithm Implementation for Searching DNA Motifs
montecarlo DNA motif gibbssampling splice
6 months ago by barslmn ★ 1.8k
2
votes
3
replies
2.5k
views
Tutorial: It's about the journey, and not the destination
R network
updated 4 months ago by 40k • written 6.5 years ago by ★ 1.2k
5
votes
3
replies
4.0k
views
Tutorial: Chip Seq Review Papers
chip-seq
updated 7 months ago by 40k • written 10.8 years ago by ▴ 80
13
votes
3
replies
11k
views
Tutorial: Plotting the coverage and depth (Y-axis) statistics of a bam file along the genome (X-axis), using Samtools, awk and R.
genome plot coverage samtools
updated 5 weeks ago by ▴ 20 • written 6.5 years ago by ★ 1.6k
15
votes
3
replies
4.4k
views
Tutorial: NCBI blast tutorial
ncbi blast
updated 5 months ago by 40k • written 7.4 years ago by 11k
6
votes
3
replies
4.3k
views
Tutorial: Principles and Workflow of 16S/18S/ITS Amplicon Sequencing
alignment sequencing RNA-seq gene
updated 6 months ago by 40k • written 4.9 years ago by ▴ 40
0
votes
3
replies
50k
views
Tutorial: Installation VMD on LINUX_64
gromacs VMD
updated 5 months ago by 40k • written 7.3 years ago by ▴ 10
7
votes
3
replies
1.7k
views
Tutorial: Automated dbSNP lookup by rsID position, plus genome build liftover
rsid hg19 liftover hg38 dbsnp
updated 5 months ago by ▴ 110 • written 13 months ago by 86k
3
votes
3
replies
2.2k
views
Tutorial: Generating count matrix for STAR counts in GDC v32.0 for RNA-Seq
GDC TCGABiolinks STAR
updated 7 months ago by 40k • written 17 months ago by ★ 3.3k
4
votes
3
replies
4.3k
views
Tutorial: How to get full taxonomy classification using taxize and myTAI
taxonomy R
updated 6 months ago by 40k • written 5.5 years ago by ★ 3.9k
2
votes
3
replies
1.8k
views
Tutorial: Help demonstrate reproducibility in bioinformatics with the GA4GH's tool execution Challenge
GA4GH Docker CWL Rabix
updated 5 months ago by 40k • written 6.6 years ago by ▴ 20
11
votes
3
replies
1.3k
views
Tutorial: Creating great documentation for bioinformatics software
Software-Documentation
updated 5 months ago by 40k • written 7.2 years ago by 7.1k
3
votes
3
replies
8.3k
views
Tutorial: High Speed Downloading of SRA, SAM and Fastq Files
fastq sam Aspera-Connect sra
updated 4 months ago by 40k • written 5.8 years ago by ▴ 100
60
votes
2
replies
7.1k
views
Tutorial: Table Of Contents To All Review Paper Compilations On Biostar
papers
updated 7 months ago by 40k • written 11.1 years ago by 98k
4
votes
2
replies
2.3k
views
Tutorial: Building mosdepth on macOS
nim mosdepth
updated 20 days ago by 134k • written 3.4 years ago by 76k
3
votes
2
replies
5.1k
views
Tutorial: Reorder Vcf Files
vcf
updated 7 months ago by 40k • written 10.4 years ago by ▴ 60
15
votes
2
replies
1.8k
views
Tutorial: Germline variant calling pipeline using Snakemake
snakemake GATK germline_variant_calling
updated 11 months ago by ▴ 810 • written 2.0 years ago by ▴ 280
1
vote
2
replies
470
views
Tutorial: How to ask computational biology questions
computational-biology
updated 3 months ago by 40k • written 3 months ago by ★ 3.4k
325 results • Page 3 of 7
Recent Votes
geom_signif() uses t-test to compare between more than 3 groups... Isn't this wrong?
Answer: Filter transcription factors
Comment: Calculation of TMB on gene level
Comment: Should I Learn Docker to Run Command Line Bioinformatics Tool?
Comment: ATAC-seq troubleshoot - Just Noise
t2t human reference genome for RNA-seq
Answer: Samtools Failing to Install through Conda
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Recent Replies
Answer: BED files by Alex Reynolds 35k
Generically via `bedmap`: ``` bedmap --echo --echo-map --count exome.bed annotations.bed > answer.bed ``` The `annotations.bed` fil…
Comment: geom_signif() uses t-test to compare between more than 3 groups... Isn't this wr by dariober 14k
It seems to me that anova followed by HSD is a more sensible approach than applying independent t-tests. Granted this is the first time I s…
Comment: BED files by barslmn ★ 1.8k
I am guessing you want the annotation files. https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/
Comment: Filter human transcription factors by Alex Reynolds 35k
Curious how redundant these TFs are. Jeff Vierstra has done some analysis on this to simplify model sets: https://www.vierstra.org/resource…
Comment: Read block operation failed with BAM file by Alex Reynolds 35k
https://github.com/samtools/htslib/pull/1676 patches a seek issue in `htslib` (upon which `samtools` and `pysam` depend)
Comment: Merging the filename with tsv files for master file by barslmn ★ 1.8k
Could you add samples from your files and your expected output.
Comment: Download an example of fully-imputed VCF files ? by barslmn ★ 1.8k
Check out the 1000 genomes project. https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/
Comment: obtaining circular RNAs' sequences from circBase by Barry Digby ★ 1.2k
Sorry my mistake! it’s been a minute since I’ve used these sites. Yes that it is common place, what is the goal of your analysis using th…
Comment: gene correlations in between two groups by ATpoint 76k
Use specialized software to analyse CRISPR/RNAi data, such as MAGeCK.
Comment: gene correlations in between two groups by edus_bioinfo ▴ 40
To be more clear, I have RNAi data from depmap with different cell lines and I separated them into two groups according to their EGFR mutat…
Comment: ATAC-seq troubleshoot - Just Noise by ATpoint 76k
You have reads, so sequencing is obviously fine. This is how the banding should look: https://kb.10xgenomics.com/hc/article_attachments/360…
Comment: Program for Overlapping DMRs (Differentially Methylated Regions) Between Groups by Basti ★ 1.7k
Do not use excel for bioinformatics purposes, using R you could use GRanges objects to find overlaps between your regions : https://www.bio…
Answer: Saving the output of LD pruning from SNPRelate package as a new GDS file by Patrick • 0
Thank you James for the response; My problem is only if I want to use the output of LD pruning in a different software, like STRUCTURE (to …
Answer: Average Coverage after Assembly (Spades) by taniapsduarte • 0
Hi, I'm running into the same issue. Did you make it work? Or did you find an alternative method? Thanks!
Answer: Can vg take MUMmer output as input? by Qi • 0
get the sv from delta and u can set them as input of vg
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