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Forum: [Meta] Use of AI
Artificial ChatGPT Intelligence Biostars AI
updated 10 minutes ago by 129k • written 2 hours ago by ★ 2.9k
0
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0
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7
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How to keep ComplexHeatmap from reordering annotations
Dendrogram HeatmapAnnotations R Heatmap ComplexHeatmap
25 minutes ago by Manuel • 0
1
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2
replies
147
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RNASeq gene labeling and mRNA filter from bulkRNA data.
RNA-Seq RSubreads
updated 1 hour ago by ▴ 100 • written 1 day ago by • 0
1
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2
replies
80
views
Random dataset and DESeq2
DESeq2
updated 2 hours ago by ★ 2.9k • written 3 hours ago by • 0
1
vote
1
reply
86
views
Network cross-validation
wgcna RNASeq Network CV
updated 3 hours ago by 2.6k • written 13 hours ago by ▴ 500
744
votes
162
replies
113k
views
101 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
training handbook
updated 5 weeks ago by 1.8k • written 6.5 years ago by 98k
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0
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31
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Differential protein expression analysis
R proteomic statistics
3 hours ago by Ribo ▴ 40
0
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1
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60
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(ERR): "index/Trinity.fa" does not exist or is not a Bowtie 2 index Exiting now ...
bowtie2 align_stats trinity
updated 2 hours ago by 129k • written 4 hours ago by ▴ 20
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2
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112
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I have one fasta file of a bacteria. Can i use to create a phylogenetic tree?
Bioinformatics WGS
8 hours ago by Mustafa • 0
0
votes
2
replies
92
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What are recommended parameters for the local protein alignment ?
protein alignment
1 hour ago by Alexander ▴ 70
0
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0
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56
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microsatellite, SSR, using Galaxy
Galaxy SSR using microsatellite
13 hours ago by m.esmaeilpour ▴ 10
0
votes
2
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163
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integrate single cell RNA sequencing data
scRNAseq single-cell
updated 16 hours ago by 2.9k • written 1 day ago by ▴ 50
0
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0
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66
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decoupleR & Transcription Factory Activity Inference: pvalue or padj?
pvalue padj decoupleR
18 hours ago by OST ▴ 10
2
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7
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307
views
How to sort gff3 according to chromosome order?
gff3 sort
updated 1 day ago by 154k • written 1 day ago by • 0
2
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3
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208
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Low mapping percentage
mapping STAR RNAseq
4 hours ago by Sib ▴ 40
0
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0
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94
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Visualization App for RNASeq Differential Expression and Enrichment Analysis
differential visualization RNASeq analysis expression enrichment
1 day ago by Mark • 0
5
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3
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211
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What does canonical transcript mean in the context of VEP
vep
updated 16 hours ago by ★ 2.9k • written 1 day ago by ▴ 720
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0
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107
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Job: Postdoctoral Research Associate in bio-ontologies and machine learning (Imageomics)
Machine-Learning PostDoc Data-Science Biology Ontology
updated 1 day ago by 39k • written 1 day ago by • 0
0
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0
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81
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calculate p value and associated z score for snp-gene pair
snp association gene pvalue
1 day ago by rheab1230 ▴ 140
0
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1
reply
99
views
Why is coordinate sort required before findng read depths?
wgs sambamba
updated 1 day ago by 39k • written 1 day ago by • 0
2
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4
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179
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bcftools "--filter-logic" flag, what + means?
bcftools vcf
updated 1 day ago by 39k • written 1 day ago by ▴ 170
3
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3
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1.8k
views
h5ad cellxgene to R
single-cell h5 cellxgene anndata R
updated 1 day ago by • 0 • written 6 months ago by ★ 1.5k
0
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0
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84
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busco id description
OrthoDB BUSCO
updated 1 day ago by 39k • written 1 day ago by • 0
0
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5
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274
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how to Construct a Newick tree file from five large fasta files
tree Newick alignment
updated 1 day ago by 21k • written 1 day ago by • 0
2
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7
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363
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What is "pident" (percentage of identical matches) in the "Diamond" protein alignment ?
protein alignment
updated 16 hours ago by ★ 2.9k • written 1 day ago by ▴ 70
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0
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93
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NMDS plotting issue
NMDS metagenomic
1 day ago by arshad1292 ▴ 90
0
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1
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116
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featurecounts not working on mirbase annotation file
usegalaxy miRNA-seq
updated 1 day ago by 129k • written 1 day ago by ▴ 90
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0
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89
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News: Generalized Linear Models (GLM) course in R
R GLM statistics
1 day ago by carlopecoraro2 ★ 2.3k
0
votes
0
replies
84
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IGV insertions
insertions IGV
1 day ago by christoph.schubart • 0
1
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0
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90
views
Bayesian network for biological data using bnlearn
bnlearn RNA-seq bayesian-network
updated 1 day ago by 39k • written 1 day ago by ▴ 10
0
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0
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80
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jellyfish options
kmer jellyfish
1 day ago by Tele • 0
0
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1
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355
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Diffbind not calling sites as differentially bound
DiffBind
updated 1 day ago by ★ 1.7k • written 9 months ago by • 0
0
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3
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140
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hardfilter error
bam recall
1 day ago by bestone ▴ 10
0
votes
1
reply
129
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Creating a local version of Clustered NR database
diamond clustered-nr blast
updated 1 day ago by 39k • written 1 day ago by • 0
0
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1
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225
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News: 7th Berlin Summer School in NGS Data Analysis (September 4-8 in Berlin)
Variant-Calling Transcriptomics RNA-Seq DNA-Seq
updated 1 day ago by 39k • written 26 days ago by 9.9k
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0
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73
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cnetplot enrichment graph to cytoscape
clusterprofiler cnetplot enrichplot
1 day ago by Omics data mining ▴ 220
0
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0
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81
views
How to extract the surrogate variables from DNA methlation Data
sva array limma methylation
updated 1 day ago by 129k • written 1 day ago by • 0
1
vote
1
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311
views
Reads with highest MAPQ values from SAM files are showing mismatches to reference sequence and IGV classified them as supplementary reads
minimap Nanopore IGV
updated 1 day ago by 129k • written 1 day ago by ▴ 20
0
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5
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230
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All combinations of two columns R
R
updated 1 day ago by 39k • written 1 day ago by • 0
0
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0
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75
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Stratified sample assignment for analysis
experimental-design stratification
updated 1 day ago by 39k • written 1 day ago by ▴ 200
0
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0
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70
views
Convert tree into bifurcation table
Tree Newick ASR Mutation
1 day ago by Alexandre • 0
0
votes
1
reply
128
views
how to call variants in haploid genome
haploid-genome
updated 1 day ago by 39k • written 1 day ago by • 0
0
votes
1
reply
125
views
Processing WES VCF for case control GWAS analysis
GWAS PLINK
updated 1 day ago by ▴ 360 • written 1 day ago by • 0
2
votes
2
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136
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How to extract haplotype data from phased bcf files
gwas vcf bcftools wgs phasing
1 day ago by Lynne-95 • 0
0
votes
4
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258
views
convert data frame with character column to data frame with integer column
r
1 day ago by atemedorri137798 • 0
0
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1
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148
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DE genes across multiple scRNAseq clusters-are they significantly enriched?
Single-cell
updated 1 day ago by 72k • written 1 day ago by • 0
4
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6
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1.5k
views
Why weblogo of biopython doesn't work?
Biopython Weblogo
updated 1 day ago by • 0 • written 9 months ago by ▴ 20
0
votes
2
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282
views
Make a BedGraph file
BedGraph RepeatMasker BED
updated 1 day ago by ▴ 100 • written 4 days ago by ▴ 10
1
vote
2
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183
views
The famous WGS dataset, Ashkenazi Trio?
wgs dataset
updated 1 day ago by • 0 • written 1 day ago by • 0
2
votes
3
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394
views
What is the best way to clean bulk RNA-seq data?
normalization TPM r
updated 1 day ago by ▴ 100 • written 5 days ago by ▴ 100
110,440 results • Page 1 of 2209
Recent Votes
Answer: I have one fasta file of a bacteria. Can i use to create a phylogenetic tree?
Comment: RNASeq gene labeling and mRNA filter from bulkRNA data.
[Meta] Use of AI
Answer: Network cross-validation
Answer: Random dataset and DESeq2
A: Single end or paired end for variant calling
Comment: Single end or paired end for variant calling
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Recent Replies
Answer: [Meta] Use of AI by GenoMax 129k
As you indicate, AI in some form or other is here to stay and we can't avoid it in our lives and on biostars. Main issue I see is the vali…
Answer: RNASeq gene labeling and mRNA filter from bulkRNA data. by rfran010 ▴ 100
featureCounts can extract this information and output a column for you during counting, presuming you input a GTF file. `extraAttributes …
Comment: What are recommended parameters for the local protein alignment ? by Alexander ▴ 70
Trying to do so ))
Comment: Help with running ATAC using Encode pipeline by rfran010 ▴ 100
The "Input files" section is details on how you can specify your fastqs in the JSON. (You specify all pipeline parameters in the JSON.) Ess…
Comment: What are recommended parameters for the local protein alignment ? by Vincent Laufer ★ 2.9k
does this mean you understand pident now and are moving forward?
Answer: Random dataset and DESeq2 by Vincent Laufer ★ 2.9k
@e38da452 Not only is this not surprising, it is the basis for an entire class of statistical techniques referred to as permutation bas…
Comment: (ERR): "index/Trinity.fa" does not exist or is not a Bowtie 2 index Exiting now by GenoMax 129k
> This generated multiple Trinity.fa files in the index folder Did the process complete successfully?
Comment: Random dataset and DESeq2 by LChart 2.6k
I don't think you've given enough detail about your approach (what's the data? are you correcting for covariates? how did you shuffle? how …
Answer: Network cross-validation by LChart 2.6k
What do you mean by "robust" in this case? Which of the following is closest to what you want to estimate: (1) Would I get a similar res…
Comment: I have one fasta file of a bacteria. Can i use to create a phylogenetic tree? by Mustafa • 0
Thank you so much ! will try them all !
Answer: I have one fasta file of a bacteria. Can i use to create a phylogenetic tree? by andres.firrincieli 3.3k
If the fasta file contains the genome sequence you can use the following: 1. GToTree (see example [here][1]) 2. [GTDB-tk][2] *de novo…
Comment: Low mapping percentage by Sib ▴ 40
Thank you for the reply @genomax . If there is not much I can do about the contamination at this stage, what is the benefit of knowing the…
Answer: integrate single cell RNA sequencing data by Hamid Ghaedi 2.9k
There are different approaches that you may choose to deal with batch correction. Harmony is one of those approaches that has been shown to…
Comment: What does canonical transcript mean in the context of VEP by Vincent Laufer ★ 2.9k
@curious - The only thing I have to add to @yokofakun 's precise answer is that, while you are considering and reading about Ensembl canoni…
Comment: Help with running ATAC using Encode pipeline by Chris ▴ 100
Thank you for the instruction! I see the beside json file we also have input file which I am confused. Because we have already defined the …
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