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196
votes
44
replies
69k
views
33 follow
Tutorial: Analysing Microarray Data In Bioconductor
microarray-analysis bioconductor
updated 5 months ago by 39k • written 10.7 years ago by 20k
6
votes
2
replies
1.2k
views
Tutorial: GSE28955 - Agilent-016436 Human miRNA Microarray 1.0
limma GPL6955 Microarray miRNA Agilent
22 months ago by Kevin Blighe 85k
0
votes
0
replies
968
views
Tutorial: Alignment-free RNA-seq Differential Gene Expression Analysis with Kallisto & Sleuth
dge kallisto rnaseq sleuth
22 months ago by mo • 0
2
votes
0
replies
2.0k
views
Tutorial: Affymetrix HTA 2.0 id conversion
biomart HTA affymetrix Affymetrix 2.0
22 months ago by Kevin Blighe 85k
45
votes
2
replies
36k
views
Tutorial: Mapping Reads With Bwa And Bowtie
bowtie bwa
updated 3 months ago by 39k • written 11.2 years ago by ▴ 540
92
votes
105
replies
36k
views
25 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 12 weeks ago by 39k • written 4.8 years ago by 85k
0
votes
0
replies
813
views
Tutorial: Event & tutorial: open software tools and AI for improving bioimaging (SLURM, containerisation)
containerisation bioimaging SLURM health
24 months ago by Erin Haskell | ELIXIR ▴ 470
1
vote
0
replies
1.0k
views
Tutorial: Slurm and parallelization
slurm
24 months ago by Juke34 7.9k
1
vote
0
replies
1.0k
views
Tutorial: How to: make Camellia sinensis var. sinensis (black tea) custom annotation files for BINGO Cytoscape
bingo cytoscape
2.0 years ago by Pratik ▴ 880
12
votes
1
reply
2.2k
views
Tutorial: PCR Primer or Primer+Probe design
pcr probe rt-pcr qpcr primer
updated 2.0 years ago by ★ 14k • written 2.0 years ago by 85k
116
votes
66
replies
41k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera fastq-dump Fastq ENA
updated 12 weeks ago by 39k • written 4.9 years ago by 73k
4
votes
0
replies
971
views
Tutorial: Long Read Genome Assembly Video Series
long-read genome-assembly
2.0 years ago by pbpanigrahi ▴ 420
0
votes
1
reply
803
views
Tutorial: Add Customized Filters in GDC
gdc
updated 2.0 years ago by 21k • written 2.0 years ago by ▴ 800
65
votes
26
replies
12k
views
11 follow
Tutorial: Generating consensus sequence from bam file
fasta consensus bam
updated 12 weeks ago by 39k • written 4.3 years ago by 16k
12
votes
20
replies
12k
views
10 follow
Tutorial: Associating VDJ clonotyping data with scRNA-seq in Seurat
single-cell RNA-Seq seurat TCR
updated 12 weeks ago by 39k • written 4.0 years ago by ★ 14k
4
votes
2
replies
2.1k
views
Tutorial: Apply beagle5.0 to make imputation and phasing under CentOS and PBS
beagle5.0 beagle
updated 12 weeks ago by 39k • written 4.0 years ago by ★ 9.3k
45
votes
14
replies
66k
views
10 follow
Tutorial: Using R in Conda
R
updated 12 weeks ago by 39k • written 2.9 years ago by ▴ 690
31
votes
9
replies
27k
views
11 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda
updated 12 weeks ago by 39k • written 2.8 years ago by ▴ 140
99
votes
16
replies
31k
views
18 follow
Tutorial: Heatmaps in R
heatmap R
updated 12 weeks ago by 39k • written 6.8 years ago by 26k
21
votes
2
replies
4.2k
views
Tutorial: Extracting genomic feature sequences from GTF/GFF files with AGAT
extract GTF GFF sequence
updated 9 months ago by ▴ 40 • written 2.1 years ago by 7.9k
31
votes
6
replies
9.5k
views
Tutorial: A simple tutorial for a complex ComplexHeatmap
clustering pam arthritis ComplexHeatmap
updated 12 weeks ago by 39k • written 3.1 years ago by 85k
78
votes
42
replies
29k
views
25 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 4 weeks ago by 39k • written 9.6 years ago by ★ 7.7k
8
votes
0
replies
2.2k
views
Tutorial: Pipes in R: An introduction and some advanced tips and tricks.
R
2.2 years ago by rpolicastro 12k
238
votes
176
replies
86k
views
73 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq Survival TCGA
updated 16 days ago by 39k • written 7.9 years ago by ★ 4.6k
6
votes
0
replies
1.7k
views
Tutorial: data.frames in R: How vectorization can save you time and heartache
R
2.2 years ago by rpolicastro 12k
8
votes
1
reply
1.1k
views
Tutorial: Split a 'linearised' (flattened) FASTA sequence into multi-line using AWK
fasta awk
updated 12 weeks ago by 39k • written 2.2 years ago by 85k
21
votes
10
replies
5.3k
views
Tutorial: Finding the significance of the overlap between 2 or more gene sets using simulation in R.
tidyverse gene R
updated 12 weeks ago by 39k • written 2.8 years ago by 12k
12
votes
2
replies
1.1k
views
Tutorial: Factors in R - How do they work, and how did I break my data?
R
updated 12 weeks ago by 39k • written 2.2 years ago by 12k
148
votes
35
replies
59k
views
33 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics next-gen
updated 3 months ago by 39k • written 10.5 years ago by ★ 1.6k
14
votes
2
replies
3.1k
views
Tutorial: Methylation Analysis Tutorial in R_part2
cancer methylation RNA-Seq R
updated 12 weeks ago by 39k • written 2.7 years ago by 2.9k
4
votes
0
replies
1.9k
views
Tutorial: Building mosdepth on macOS
nim mosdepth
updated 12 weeks ago by 39k • written 3.1 years ago by 73k
16
votes
7
replies
13k
views
Tutorial: Integrating VDJ sequencing data with Seurat
VDJ Seurat sc-RNAseq clonotyping
updated 12 weeks ago by 39k • written 4.0 years ago by ▴ 310
277
votes
33
replies
95k
views
25 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 3 months ago by 39k • written 9.6 years ago by 20k
5
votes
0
replies
3.7k
views
Tutorial: Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates without alignment), mutate (create mutant genomes) and other miscellaneou…
bbmap
updated 12 weeks ago by 39k • written 2.4 years ago by 130k
10
votes
0
replies
5.0k
views
Tutorial: Yes .. BBMap can do that! - Part II randomreads (read simulation), demuxbyname/filterbyname, bbsplit (read binning/decontamination) and pileup (cover…
bbmap
updated 12 weeks ago by 39k • written 2.4 years ago by 130k
10
votes
0
replies
3.1k
views
Tutorial: Yes .. BBMap can do that! - Part I : bbmap (aligner), bbduk (scan/trim), repair (fix PE reads) and reformat (format conversions)
bbmap
updated 12 weeks ago by 39k • written 2.4 years ago by 130k
11
votes
1
reply
2.3k
views
Tutorial: Guidelines for the computational analysis of single-cell RNA sequencing data
scRNA-seq
updated 12 weeks ago by 39k • written 2.4 years ago by ★ 23k
40
votes
9
replies
11k
views
10 follow
Tutorial: Resources for flow cytometry bioinformatics
single-cell flow-cytometry
updated 3 months ago by 39k • written 9.2 years ago by ★ 1.9k
0
votes
1
reply
2.5k
views
Tutorial: Getting the lineage of an organism from NCBI taxonomy data
biosql python taxonomy
updated 12 weeks ago by 39k • written 4.8 years ago by ▴ 310
76
votes
13
replies
14k
views
12 follow
Tutorial: Exploring cancer mutation data portals
TCGA Cancer ICGC Data-Portal Mutation
updated 20 months ago by 39k • written 9.0 years ago by 19k
6
votes
10
replies
4.5k
views
Tutorial: Differentially methylated regions: Easy & Fast Identification and ANnoTation
DMR dna-methylation
updated 12 weeks ago by 39k • written 5.3 years ago by ▴ 360
43
votes
6
replies
11k
views
Tutorial: Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
ensembl maf tcga vcf
updated 3 months ago by 39k • written 9.4 years ago by 5.9k
5
votes
3
replies
4.7k
views
Tutorial: bam2rpkm by bedtools
bam RNA-Seq bedtools rpkm
updated 12 weeks ago by • 0 • written 5.6 years ago by ▴ 130
16
votes
11
replies
7.5k
views
Tutorial: How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking
meta how-to documentation
12 weeks ago by Ram 39k
45
votes
28
replies
7.4k
views
9 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation meta how-to
22 days ago by Ram 39k
101
votes
6
replies
23k
views
6 follow
Tutorial: Creating workflows with snakemake and conda
workflow snakemake conda
updated 12 weeks ago by 39k • written 4.8 years ago by 16k
18
votes
40
replies
16k
views
16 follow
Tutorial: Easy way to run easily orthoMCL (Copy & paste)
all-v-all orthomcl
updated 12 weeks ago by 39k • written 7.0 years ago by ▴ 170
23
votes
4
replies
6.5k
views
Tutorial: Using EnrichedHeatmap for visualization of NGS experiments
heatmap chip-seq atac-seq EnrichedHeatmap
updated 12 weeks ago by 39k • written 3.8 years ago by 73k
15
votes
4
replies
4.2k
views
Tutorial: RNASeq tutorial for gene differential expression analysis
Transcriptomics bioconductor RNA-Seq R
updated 12 weeks ago by 39k • written 2.9 years ago by ▴ 310
26
votes
0
replies
2.1k
views
Tutorial: Resources / databases for clinical interpretation of cancer variants
interpretation cancer annotation variant
updated 12 weeks ago by 39k • written 3.7 years ago by 19k
358 results • Page 2 of 8
Recent Votes
Answer: Solving environment: failed with initial frozen solve. Retrying with flexible so
Answer: Solving environment: failed with initial frozen solve. Retrying with flexible so
Comment: Solving environment: failed with initial frozen solve. Retrying with flexible so
Comment: GISTIC from ASCAT
Answer: hisat2-align exited with value 1
Answer: hisat2-align exited with value 1
vg rna index
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Recent Awards • All
Scholar to GenoMax 130k
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Recent Replies
Comment: multiqc: group samples by population + boxplot ? by Pierre Lindenbaum 155k
It worked by parsing a first run of multiqc, extract the data from the sanitised data , create a SVG plot with R, include the SVG into a fi…
Comment: Solving environment: failed with initial frozen solve. Retrying with flexible so by Ahmed ▴ 10
thanks, bro I get the solve of my problem by installing new environment and reinstalling samtools software again.
Comment: Solving environment: failed with initial frozen solve. Retrying with flexible so by Ahmed ▴ 10
Thanks for telling me that, and i apologize for bad explanation because I am beginner user with the site!
Comment: amrfinder not working on loop? by Pierre Lindenbaum 155k
what is the output of the following commands: ls -lah '/home/bvs/neelam/AMRFINDER_hypo/hypothetical_analysis/P_aeruginosa_RP73.fasta' …
Comment: amrfinder not working on loop? by GenoMax 130k
> Cannot open file > '/home/bvs/neelam/AMRFINDER_hypo/hypothetical_analysis/P_aeruginosa_RP73.fasta' Looks like either the file path is in…
Comment: R ggplot by Ram 39k
Is "R ggplot" the most concise/descriptive title you can use?
Answer: Solving environment: failed with initial frozen solve. Retrying with flexible so by Ram 39k
1. `bioconda` is a conda channel, not a command. I'm surprised it executes some sort of binary - what is the output of `alias bioconda` and…
Comment: Solving environment: failed with initial frozen solve. Retrying with flexible so by Ram 39k
Use proper tags - in your previous post, you pasted the question text in the tag field and here, your tag is `nothing`. Use relevant tags (…
Comment: hisat2-align exited with value 1 by Ahmed ▴ 10
thanks man <3 you saved me!!
Comment: no output from GATK CombineGVCFs by Pierre Lindenbaum 155k
> The number of gVCFs in the list has a hard limit no, I don't think so. But if you have 10000 VCFs, you should combine 100x100 VCFS and …
Comment: novel miRNA naming(annotation) by kuttibiotech2009 ▴ 30
Do you have any idea about it?. I also want to do the same.
Answer: Identify similarly mapped reads in BAM/SAM? by Pierre Lindenbaum 155k
bedtools bamtobed -i in.bam | datamash -g 1,2,3 collapse 4
Comment: GISTIC from ASCAT by Hyper_Odin ▴ 290
Also, I would like to add that we cannot use ASCAT output for GISTIC input...since GISTIC expects all the chromosomes in the input file eve…
Comment: GISTIC from ASCAT by Hyper_Odin ▴ 290
Hi, Ram thanks for the help...I figured out the issue. somehow I had duplicate files in the folder which caused the issue.
Answer: multiqc: group samples by population + boxplot ? by Phil Ewels ★ 1.2k
You can't group and make boxplots as you describe, probably your best bet is to use the [highlight tool][1] in the report (especially if yo…
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