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323 results • Page 1 of 7
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277
votes
39
replies
168k
views
29 follow
Tutorial: How to download raw sequence data from GEO/SRA
fastq SRA bam GEO
updated 10 weeks ago by 39k • written 8.8 years ago by 20k
277
votes
33
replies
94k
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
238
votes
176
replies
85k
views
73 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq Survival TCGA
updated 11 days ago by 39k • written 7.8 years ago by ★ 4.6k
82
votes
21
replies
74k
views
13 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools samtools htslib
updated 3 months ago by ★ 3.0k • written 4.9 years ago by ▴ 540
196
votes
44
replies
69k
views
33 follow
Tutorial: Analysing Microarray Data In Bioconductor
microarray-analysis bioconductor
updated 4 months ago by 39k • written 10.7 years ago by 20k
74
votes
13
replies
66k
views
10 follow
Tutorial: Machine Learning For Prediction of Relapse in Cancer - Part 2 - Building A Random Forest Classifier
r cancer classification
updated 7 months ago by 39k • written 9.5 years ago by ★ 1.2k
45
votes
14
replies
65k
views
10 follow
Tutorial: Using R in Conda
R
updated 11 weeks ago by 39k • written 2.9 years ago by ▴ 690
26
votes
10
replies
63k
views
9 follow
Tutorial: Installing an updated R version (>=4.0) using conda
software-error R
updated 12 weeks ago by 39k • written 2.2 years ago by ★ 1.3k
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
80
votes
2
replies
54k
views
Tutorial: How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 3 months ago by 39k • written 9.9 years ago by 11k
145
votes
34
replies
52k
views
17 follow
Tutorial: Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
music cancer tcga mutation maf
updated 3 months ago by 39k • written 10.1 years ago by 5.9k
0
votes
3
replies
48k
views
Tutorial: Installation VMD on LINUX_64
gromacs VMD
updated 8 weeks ago by 39k • written 7.0 years ago by ▴ 10
65
votes
9
replies
48k
views
7 follow
Tutorial: Reference Assembly - Mapping Reads To A Reference Genome
reference samtools mapping bwa
updated 3 months ago by 39k • written 9.9 years ago by ★ 3.0k
146
votes
69
replies
44k
views
19 follow
Tutorial: Network plot from expression data in R using igraph
microarray RNA-Seq R network
updated 9 weeks ago by ▴ 10 • written 5.5 years ago by 85k
51
votes
19
replies
42k
views
6 follow
Tutorial: Visualizing Chip-Seq Data Using Ucsc [Bigwig]
visualization bigwig chip-seq rna-seq
updated 3 months ago by 39k • written 11.1 years ago by 11k
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 11 weeks ago by 39k • written 4.9 years ago by 72k
60
votes
52
replies
40k
views
23 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
plotly R volcano-plot
updated 11 weeks ago by 39k • written 6.7 years ago by ★ 3.3k
58
votes
25
replies
37k
views
15 follow
Tutorial: Protocol To Downlad TCGA Data From GDC
GDC methylation TCGA
updated 11 weeks ago by 39k • written 6.9 years ago by ★ 9.3k
92
votes
105
replies
36k
views
25 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 11 weeks ago by 39k • written 4.8 years ago by 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
94
votes
25
replies
31k
views
11 follow
Tutorial: Fastq Quality Control Shootout
quality qc trimming fastq
updated 3 months ago by 39k • written 10.7 years ago by 98k
89
votes
19
replies
31k
views
12 follow
Tutorial: Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
microarray bioconductor expression classification
updated 3 months ago by 39k • written 9.6 years ago by 20k
99
votes
16
replies
30k
views
18 follow
Tutorial: Heatmaps in R
heatmap R
updated 11 weeks ago by 39k • written 6.8 years ago by 26k
130
votes
123
replies
30k
views
23 follow
Tutorial: Survival analysis with gene expression
cox gene-expression survival-analysis geo
updated 10 weeks ago by ★ 1.1k • written 4.6 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 27 days ago by 39k • written 9.6 years ago by ★ 7.7k
82
votes
28
replies
28k
views
19 follow
Tutorial: How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor GenVisR Graphics R
updated 3 months ago by 39k • written 7.2 years ago by 20k
1
vote
1
reply
27k
views
Tutorial: Docker denied: requested access to the resource is denied
docker
updated 10 months ago by ★ 2.9k • written 10 months ago by ▴ 10
99
votes
8
replies
27k
views
8 follow
Tutorial: Guide to TCGA data
cancer RNA-Seq clinical TCGA
updated 8 weeks ago by 39k • written 7.3 years ago by ★ 1.1k
31
votes
12
replies
27k
views
7 follow
Tutorial: So What Does The Sequence Duplication Rate Really Mean In A Fastqc Report
quality-control fastqc
updated 3 months ago by 39k • written 9.6 years ago by 98k
31
votes
9
replies
26k
views
11 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda
updated 11 weeks ago by 39k • written 2.8 years ago by ▴ 140
70
votes
26
replies
25k
views
15 follow
Tutorial: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 3 months ago by 39k • written 9.3 years ago by 98k
67
votes
6
replies
25k
views
7 follow
Tutorial: Rna-Seq Review Papers
RNA-seq papers
updated 3 months ago by 39k • written 10.8 years ago by 98k
72
votes
60
replies
24k
views
16 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes PLINK PCA VCF
updated 3 months ago by 39k • written 5.7 years ago by 85k
101
votes
6
replies
23k
views
6 follow
Tutorial: Creating workflows with snakemake and conda
workflow snakemake conda
updated 11 weeks ago by 39k • written 4.8 years ago by 16k
51
votes
3
replies
22k
views
Tutorial: Sam File Format - Lesser Known Tips And Tricks
sam
updated 3 months ago by 39k • written 10.4 years ago by ▴ 300
42
votes
16
replies
21k
views
15 follow
Tutorial: Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.
GISTIC varscan2 CNV copy-number
updated 10 months ago by 39k • written 7.7 years ago by ★ 2.3k
30
votes
6
replies
21k
views
Tutorial: Transforming And Manipulating Color Space Reads
conversion solid
updated 8 months ago by 39k • written 11.1 years ago by 98k
10
votes
5
replies
19k
views
Tutorial: Y-DNA and mtDNA Haplogroup Predictor
haplogroup
updated 11 weeks ago by 39k • written 4.9 years ago by ★ 9.3k
59
votes
43
replies
18k
views
18 follow
Tutorial: Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
pbalign pacbio arrow smrt-limk
updated 11 weeks ago by 39k • written 5.7 years ago by ★ 1.4k
34
votes
15
replies
18k
views
12 follow
Tutorial: TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen GDC R TCGA
updated 11 weeks ago by 39k • written 6.7 years ago by ▴ 310
42
votes
2
replies
17k
views
Tutorial: Sequencing Technology Review Papers
sequencing papers
updated 3 months ago by 39k • written 10.8 years ago by 98k
39
votes
6
replies
17k
views
Tutorial: Creating chromosome karyotype plot with R and ggplot2
ggplot2 R chromosome karyotype
updated 19 days ago by 39k • written 5.8 years ago by ★ 3.3k
76
votes
70
replies
16k
views
18 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
updated 11 weeks ago by 39k • written 5.3 years ago by 85k
83
votes
21
replies
16k
views
16 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 12 weeks ago by 39k • written 2.6 years ago by 2.9k
18
votes
40
replies
16k
views
16 follow
Tutorial: Easy way to run easily orthoMCL (Copy & paste)
all-v-all orthomcl
updated 11 weeks ago by 39k • written 6.9 years ago by ▴ 170
83
votes
34
replies
16k
views
22 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment R pathway active-subnetwork
updated 9 days ago by • 0 • written 5.0 years ago by ★ 1.3k
72
votes
48
replies
16k
views
15 follow
Tutorial: For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
ngs alignment bwa
updated 3 months ago by 39k • written 10.3 years ago by 33k
34
votes
17
replies
15k
views
12 follow
Tutorial: Machine Learning For Cancer Classification - Part 3 - Predicting With A Random Forest Classifier
machine-learning classification
updated 4 weeks ago by 129k • written 9.5 years ago by 20k
30
votes
14
replies
15k
views
8 follow
Tutorial: Installation of the MuSiC suite on unsupported Linux distributions
genome-music linux smg
updated 3 months ago by 39k • written 10.3 years ago by 5.9k
73
votes
14
replies
14k
views
15 follow
Tutorial: List Of Bioinformatics Books
books
updated 3 months ago by 39k • written 10.0 years ago by 9.6k
323 results • Page 1 of 7
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Answer: How To Predict Pseudogenes In A Genome
A: How To Predict Pseudogenes In A Genome
A: How To Predict Pseudogenes In A Genome
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How To Predict Pseudogenes In A Genome
C: parsing fasta file
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Teacher to antonioggsousa 2.8k
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Recent Replies
Answer: Installation of PPFinder by GenoMax 129k
Since the software is still [**listed on the Brent lab**][1] website your best bet would be to email the investigator and ask that they fix…
Comment: How to calculate TPM from featureCounts output by rpolicastro 12k
If you want to go that route, yes.
Comment: Difference between USCS exon coordinates and ensembl by ATpoint 72k
What did you download from UCSC? 1-off usually means one file is zero-based and the other 1-based. BED files from UCSC are 0-based, Ensembl…
Comment: Alignment of case vs. control from different origin by sativus • 0
Thank you kindly for the explanation, it is highly appreciated. I suppose i was a bit confused as you quite often see people validating the…
Answer: Gene enrichment analysis by nux ▴ 10
Hello. For this you have to select 'hyper' as your method and then provide a complete list of genes which both include the candidate and no…
Comment: CNNScoreVariants Error by bestone ▴ 10
Thank you for replying I updated it worked but it gives another Error A USER ERROR has occurred: Invalid argument ' -V'.
Comment: Impute haplotypes (ImputePipelinePlugin) execution error - PHG by jrodrigu • 0
Thank you so much. I made the suggested changes. However, I still have the same problem. Please check the new log file. https://github.c…
Comment: Getting same value for start and end position, "DNA methylation" by ATpoint 72k
That's a comment, not an answer, please use `ADD COMMENT`.
Comment: Getting same value for start and end position, "DNA methylation" by bioinfo_ga ▴ 50
Are you working on bisulphite kind of data or chipseq ????
Answer: How to calculate TPM from featureCounts output by bioinfo_ga ▴ 50
hi , You can use a python package rnanorm [https://pypi.org/project/rnanorm/]. The input required are your read count values from feature …
Comment: How to split a scRNA reads BAM or FASTQ file to a separate file for each cell by by biofalconch ▴ 580
Hey, if you arelady have the barcodes, you could use samtools `samtools view -h -b -f CB:Z:TAAGAGATCCTATGTT > TAAGAGATCCTATGTT.bam` Hope…
Answer: How to split a scRNA reads BAM or FASTQ file to a separate file for each cell by by biofalconch ▴ 580
Here is a code that should work, but just like everyone else in the comments I'm a little confused why would you need to separate them: …
Comment: Make a BedGraph file by kirillkirilenko ▴ 10
It works, thank you!
Comment: CNNScoreVariants Error by Pierre Lindenbaum 154k
check you have a complete environment for GATK , including the python module "keras". https://gatk.broadinstitute.org/hc/en-us/articles/360…
Comment: How to split a scRNA reads BAM or FASTQ file to a separate file for each cell by by Cathal • 0
Did you have any luck in splitting the BAM file based on the 10x cell barcode? I would like to split a BAM file based to only include 5 spe…
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