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383 results • Page 1 of 8
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238
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90k
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Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq Survival TCGA
updated 6 months ago by 41k • written 8.3 years ago by ★ 4.7k
132
votes
123
replies
34k
views
23 follow
Tutorial: Survival analysis with gene expression
cox gene-expression survival-analysis geo
updated 8 months ago by ★ 1.1k • written 5.1 years ago by 86k
95
votes
105
replies
41k
views
25 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 8 months ago by 41k • written 5.2 years ago by 86k
148
votes
70
replies
48k
views
20 follow
Tutorial: Network plot from expression data in R using igraph
microarray RNA-Seq R network
updated 3 months ago by ▴ 260 • written 6.0 years ago by 86k
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
117
votes
66
replies
44k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera fastq-dump Fastq ENA
updated 8 months ago by 41k • written 5.4 years ago by 78k
73
votes
60
replies
26k
views
16 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes PLINK PCA VCF
updated 9 months ago by 41k • written 6.2 years ago by 86k
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
72
votes
48
replies
17k
views
15 follow
Tutorial: For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
ngs alignment bwa
updated 9 months ago by 41k • written 10.8 years ago by 33k
90
votes
48
replies
31k
views
29 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 25 days ago by 41k • written 10.1 years ago by ★ 7.8k
196
votes
44
replies
70k
views
33 follow
Tutorial: Analysing Microarray Data In Bioconductor
microarray-analysis bioconductor
updated 10 months ago by 41k • written 11.2 years ago by 20k
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
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
282
votes
39
replies
176k
views
29 follow
Tutorial: How to download raw sequence data from GEO/SRA
fastq SRA bam GEO
updated 8 months ago by 41k • written 9.3 years ago by 20k
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
83
votes
34
replies
17k
views
22 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment R pathway active-subnetwork
updated 6 months ago by • 0 • written 5.4 years ago by ★ 1.3k
146
votes
34
replies
53k
views
17 follow
Tutorial: Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
music cancer tcga mutation maf
updated 9 months ago by 41k • written 10.6 years ago by 6.0k
288
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
10
votes
31
replies
9.9k
views
10 follow
Tutorial: OrthoMCL installation on Ubuntu Linux
ubuntu orthomcl mysql linux
updated 4 weeks ago by • 0 • written 5.9 years ago by ▴ 320
14
votes
31
replies
6.0k
views
6 follow
Tutorial: gene set filter/selection for training ab initio annotation tools
geneset genome gene abinitio
updated 8 months ago by 41k • written 4.3 years ago by 8.4k
48
votes
30
replies
9.3k
views
11 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation meta how-to
updated 28 days ago by 78k • written 7.7 years ago by 41k
84
votes
29
replies
30k
views
20 follow
Tutorial: How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor GenVisR Graphics R
updated 4 months ago by • 0 • written 7.7 years ago by 20k
65
votes
26
replies
13k
views
11 follow
Tutorial: Generating consensus sequence from bam file
fasta consensus bam
updated 8 months ago by 41k • written 4.7 years ago by 16k
71
votes
26
replies
27k
views
15 follow
Tutorial: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 9 months ago by 41k • written 9.8 years ago by 99k
64
votes
26
replies
13k
views
7 follow
Tutorial: Parallel processing in R
biocparallel mclapply foreach R
updated 8 months ago by 41k • written 6.2 years ago by 86k
58
votes
25
replies
39k
views
15 follow
Tutorial: Protocol To Downlad TCGA Data From GDC
GDC methylation TCGA
updated 8 months ago by 41k • written 7.3 years ago by ★ 9.3k
137
votes
25
replies
81k
views
14 follow
Tutorial: Piping With Samtools, Bwa And Bedtools
unix samtools bwa bedtools
updated 20 months ago by 41k • written 11.6 years ago by ★ 4.2k
95
votes
25
replies
32k
views
11 follow
Tutorial: Fastq Quality Control Shootout
quality qc trimming fastq
updated 9 months ago by 41k • written 11.2 years ago by 99k
18
votes
22
replies
8.4k
views
10 follow
Tutorial: Create de novo repeat library
de-novo repeat annotation
updated 9 weeks ago by ▴ 20 • written 4.0 years ago by 8.4k
88
votes
22
replies
83k
views
14 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools samtools htslib
updated 4 months ago by • 0 • written 5.3 years ago by ▴ 580
84
votes
21
replies
20k
views
16 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 8 months ago by 41k • written 3.1 years ago by 3.1k
142
votes
21
replies
29k
views
12 follow
Tutorial: A few words for R beginners
Swirl R
updated 19 months ago by 41k • written 9.0 years ago by ★ 1.6k
12
votes
20
replies
13k
views
10 follow
Tutorial: Associating VDJ clonotyping data with scRNA-seq in Seurat
single-cell RNA-Seq seurat TCR
updated 8 months ago by 41k • written 4.5 years ago by ★ 16k
47
votes
19
replies
13k
views
8 follow
Tutorial: Fastq Quality Control And Reporting - Aka Fastqc Versus The New Contenders
quality-control fastqc
updated 10 months ago by 41k • written 10.8 years ago by 99k
8
votes
19
replies
13k
views
9 follow
Tutorial: A:orthomcl with local mysql server on linux server, complete install
mysql orthomcl
updated 8 months ago by 41k • written 9.0 years ago by ▴ 600
42
votes
19
replies
7.6k
views
8 follow
Tutorial: Designing Command-Line Interfaces (Clis) For Scientific Software
software
updated 9 months ago by 41k • written 10.7 years ago by 4.1k
23
votes
19
replies
6.4k
views
10 follow
Tutorial: MutScan: Detect important mutations by scanning FastQ files directly
fastq mutation cancer target
updated 7 months ago by 41k • written 7.2 years ago by ★ 2.5k
53
votes
19
replies
43k
views
6 follow
Tutorial: Visualizing Chip-Seq Data Using Ucsc [Bigwig]
visualization bigwig chip-seq rna-seq
updated 9 months ago by 41k • written 11.6 years ago by 11k
90
votes
19
replies
31k
views
12 follow
Tutorial: Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
microarray bioconductor expression classification
updated 9 months ago by 41k • written 10.1 years ago by 20k
26
votes
17
replies
7.3k
views
8 follow
Tutorial: virtualenv - running Python based software in isolation
python virtualenv
updated 14 months ago by 41k • written 9.3 years ago by 6.0k
35
votes
17
replies
16k
views
12 follow
Tutorial: Machine Learning For Cancer Classification - Part 3 - Predicting With A Random Forest Classifier
machine-learning classification
updated 6 months ago by 136k • written 10.0 years ago by 20k
12
votes
17
replies
2.6k
views
Tutorial: How to find the mapping percentages for data deposited in the Zaire ebolavirus bioproject from the 2014 outbreak
ebola bwa
updated 11 months ago by 41k • written 8.5 years ago by 99k
8
votes
17
replies
2.9k
views
Tutorial: Simple approach to RNA-seq (T-Bioinfo platform)
alignment next-gen-sequencing RNA-seq
updated 15 months ago by 41k • written 8.1 years ago by ▴ 340
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
42
votes
16
replies
23k
views
15 follow
Tutorial: Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.
GISTIC varscan2 CNV copy-number
updated 15 months ago by 41k • written 8.2 years ago by ★ 2.4k
34
votes
15
replies
6.0k
views
6 follow
Tutorial: How to do data cleaning for VCF genetic file
vcf
updated 8 months ago by 41k • written 4.4 years ago by ★ 9.3k
63
votes
15
replies
13k
views
Tutorial: Which human reference genome should I use?
assembly genome alignment
updated 6 months ago by 41k • written 5.1 years ago by 16k
34
votes
15
replies
19k
views
12 follow
Tutorial: TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen GDC R TCGA
updated 8 months ago by 41k • written 7.1 years ago by ▴ 310
25
votes
15
replies
8.6k
views
8 follow
Tutorial: Syllabus To Learn Bioinformatics From Online Video Resources
course training mooc
updated 9 months ago by 41k • written 10.9 years ago by 9.7k
7
votes
14
replies
3.2k
views
6 follow
Tutorial: Install required dependencies for GATK4 on remote server without root privilege
gatk
updated 13 months ago by • 0 • written 21 months ago by ▴ 30
383 results • Page 1 of 8
Recent Votes
Answer: featureCounts results: low rate of 'Successfully assigned alignments'
The Biostar Herald for Monday, November 27, 2023
Comment: use bioservices.UniProt (python) to map uniprot accession to [multiple] ensembl
Answer: Best practices for unstranded sequences in featureCounts
Answer: DEseq2 input
Comment: Filter out ALT contigs from CRAM
Answer: Bowtie mapping for single_end read
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Popular Question to Hamtaro ▴ 10
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Recent Replies
Comment: Construction of single sequence assembly out of contigs by analyst ▴ 10
I have found dedup.sh script of bbmap tool that removes duplicated sequences. Also there is a seqtk tool. Is it safe to remove duplicated s…
Comment: featureCounts results: low rate of 'Successfully assigned alignments' by Hamtaro ▴ 10
Thank you for your reply. I how can I identify why I have soo many multimapping reads? The samples comes from blood from patients under d…
Comment: Construction of single sequence assembly out of contigs by analyst ▴ 10
Honestly I have not assessed duplication after assembly. However I used trimmomatic for data filtration before assembly. Trimmomatic param…
Answer: featureCounts results: low rate of 'Successfully assigned alignments' by kvn95ss ▴ 20
I could see the following clues from - hisat2 - ```23026867 (61.37%) aligned concordantly >1 times``` And from featureCounts - ``` Mu…
Comment: CPTAC data, download, merge by Mohita ▴ 50
I am also facing the same problem. I will be grateful if you help me out for this.
Comment: Circular genome browser by giammafer ▴ 20
Thank you very much for organising the 'awesome-genome-visualization' collection. I searched in your database before I made this question …
Answer: Mapping quality in `vg giraffe` by Xian ▴ 30
You can find a complete definition of how giraffe finds mapq's in the supplement of the paper: https://www.science.org/doi/10.1126/science.…
Comment: Construction of single sequence assembly out of contigs by Michael 53k
This looks actually quite like an "improvement", if it is one. Whether you use additional methods or not, the name of the software has been…
Answer: Protein Database by Elisabeth Gasteiger ★ 2.3k
Please don't hesitate to contact the UniProt helpdesk (https://www.uniprot.org/contact) if you need help with any query that would allow yo…
Comment: Best practices for unstranded sequences in featureCounts by Enrique • 0
Thank you so much. Well, it’s not my intention to resolve my problem only with featureCounts, but I want to know the best arguments in that…
Comment: I made an error when using metawrap to binning by alice005201314 • 0
Also, I checked the output file and did not find the presence of the tmp-samtools.0000.bam file, which appears to be a temporary file that …
Comment: Find Genes in Homer Analysis that have the enriched Motif by je71xusa • 0
I input a list of gene names like here http://homer.ucsd.edu/homer/microarray/index.html
Comment: I made an error when using metawrap to binning by alice005201314 • 0
The paragraph at the end of the log file may be the problem [M::mem_pestat] skip orientation RR as there are not enough pairs [M::…
Comment: I made an error when using metawrap to binning by mixiaoluo88 • 0
You should post some log file to help me understand your situation. By the way, have you checked the size of "bin_out/work_files/tmp-samtoo…
Answer: I made an error when using metawrap to binning by colindaven 5.7k
Check that the bam file exists at bin_out/work_files/tmp-samtools.0000.bam Also check the file has a header samtools view -H bi…
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