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144 results • Page 1 of 3
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3
votes
16
replies
9.9k
views
combining z-scores into a single z-score value
excel R statistics
updated 5 days ago by 39k • written 4.2 years ago by ▴ 60
1
vote
7
replies
5.6k
views
Human reference files in HG38 GATK resource bundle
VCF
updated 6 days ago by ★ 3.1k • written 5.3 years ago by ▴ 940
7
votes
7
replies
4.4k
views
RNA-Seq time series analysis using a DESeq2 spline approach yields far too many significant genes
splines DESeq2 time-series RNA-Seq
updated 5 days ago by 39k • written 4.4 years ago by ▴ 80
1
vote
5
replies
3.6k
views
Time-series or pairwise comparison EdgeR - what's more suited?
DGE-analysis Time-series pairwise
updated 5 days ago by 39k • written 6.8 years ago by ▴ 470
1
vote
1
reply
3.1k
views
Problem with PGDSpider v 2.1.0.2
alignment
updated 4 days ago by ▴ 20 • written 7.0 years ago by ▴ 10
1
vote
1
reply
2.6k
views
Comparing time series expression data
time-series gene-expression
updated 5 days ago by 39k • written 5.8 years ago by ▴ 180
0
votes
3
replies
2.4k
views
Generate GTF/GFF file (coordinates) from a FASTA annotated file.
Assembly genome
updated 2 days ago by 39k • written 3.7 years ago by • 0
1
vote
5
replies
2.3k
views
Calculating distance matrix of RNA-seq data
Dynamic-Time-Warping R time-series
updated 5 days ago by 39k • written 5.2 years ago by ★ 4.2k
4
votes
7
replies
2.2k
views
low bootstrap value?
phylogeny genome alignment
updated 4 days ago by 39k • written 4.0 years ago by ▴ 100
3
votes
12
replies
2.1k
views
What is NCBI Gene ID, where to find it and how to convert to entrez ID?
RNA-Seq
updated 3 days ago by ▴ 90 • written 3.7 years ago by ▴ 10
2
votes
1
reply
1.8k
views
How do I apply a patch to hg38?
reference human freeze hg38 patch
updated 3 days ago by 21k • written 5.6 years ago by • 0
0
votes
0
replies
1.7k
views
Artificial Neural Networks applied to environmental data
artificial-neural-networks time-series ANN
updated 5 days ago by 39k • written 8.6 years ago by ▴ 10
1
vote
1
reply
1.6k
views
Bioinformatics tools for Plasmid detection
short-read plasmid
updated 3 days ago by 39k • written 3.9 years ago by ▴ 10
4
votes
8
replies
1.6k
views
How to extract promoter sequences from a plant draft genome?
promoter genome
updated 2 days ago by 39k • written 3.7 years ago by ▴ 100
4
votes
6
replies
1.5k
views
Why weblogo of biopython doesn't work?
Biopython Weblogo
updated 3 days ago by • 0 • written 9 months ago by ▴ 20
1
vote
4
replies
1.5k
views
Time series event recurrence comparison
recurrence time-series
updated 5 days ago by 39k • written 6.7 years ago by 10k
5
votes
4
replies
1.5k
views
Detection of DE genes among different tissues of an organism during time - RNA seq
detection DE-genes multi-treatments time-series
updated 5 days ago by 39k • written 6.9 years ago by ▴ 720
1
vote
0
replies
1.3k
views
NCBI Taxon ID to IMG Genome IDs
taxon html
updated 3 days ago by 39k • written 3.9 years ago by ▴ 20
0
votes
0
replies
1.3k
views
Cuffdiff with 2 conditions and time series
cuffdiff time-series RNA-Seq transcriptome
updated 5 days ago by 39k • written 6.2 years ago by • 0
2
votes
3
replies
1.2k
views
mutational signatures in different tumor samples
somatic mutation mutational signature
updated 3 days ago by ★ 2.9k • written 4.4 years ago by ▴ 20
0
votes
1
reply
1.2k
views
Best tool for bacterial genomic island prediction?
genome genomic-island
updated 4 days ago by 39k • written 4.0 years ago by ▴ 100
0
votes
0
replies
1.1k
views
EDGE microarray time series analysis fit_models() ERROR
microarray time-series
updated 5 days ago by 39k • written 5.4 years ago by ▴ 10
3
votes
7
replies
1.1k
views
Find 3'UTRs for species
Assembly alignment
updated 2 days ago by 39k • written 3.8 years ago by ▴ 110
2
votes
6
replies
1.0k
views
Time series RNA seq design query
RNA-seq time-series deseq2
updated 5 days ago by 39k • written 18 months ago by • 0
0
votes
0
replies
933
views
Where can I find, which yeast genes definitely have similar functions?
gene functional-genomics RNA-Seq time-series
updated 5 days ago by 39k • written 6.2 years ago by ▴ 30
0
votes
1
reply
873
views
Masters in Bioinformatics
masters structural-bioinformatics assistantship
updated 3 days ago by 39k • written 3.9 years ago by ▴ 10
0
votes
0
replies
866
views
Error processing Hi-data using HiCUP
NGS HiCUP Hi-C
updated 4 days ago by 39k • written 4.0 years ago by ▴ 40
0
votes
1
reply
849
views
Get publication counts per gene per year
eutilities
updated 5 days ago by 39k • written 4.2 years ago by ▴ 60
0
votes
0
replies
838
views
Time series analysis for RNA-seq paired samples
TimeSeriesExperiment RNA-Seq time-series
updated 5 days ago by 39k • written 3.3 years ago by • 0
0
votes
1
reply
811
views
Filtering for homozygous reference alleles
SNP sequence genome
updated 2 days ago by 39k • written 3.7 years ago by ▴ 30
0
votes
1
reply
803
views
Segmentation method in CNV
CNV sequencing
updated 5 days ago by 39k • written 4.1 years ago by • 0
0
votes
0
replies
796
views
Simulating Time Course RNA-Seq Data With Polyester
Time-Course RNA-Seq
updated 5 days ago by 39k • written 4.0 years ago by ▴ 10
0
votes
4
replies
789
views
Detecting Biomarkers from Time Series Gene Epression data
Time-Series Gene-Expression Biomarkers
updated 5 days ago by 39k • written 3.1 years ago by • 0
0
votes
1
reply
762
views
Can I send my PyMol results to a web-page as a result for a submitted query? If not, how can I get a 3d render of a protein as a result for a user su…
protein-structure pymol protein pdb python
updated 5 days ago by 21k • written 9 days ago by • 0
0
votes
1
reply
754
views
Where can I find Time Series Multi-Omics human cancer datasets
multi-omics cancer time-series
updated 5 days ago by 39k • written 3.2 years ago by • 0
0
votes
1
reply
749
views
plasmid spades R1/R2 files?
plasmid sequencing
updated 2 days ago by 39k • written 3.7 years ago by • 0
2
votes
0
replies
724
views
Why are there multiple bax/fastq files associated with my PacBio run?
genome PacBio WGS sequencing
updated 5 days ago by 39k • written 4.1 years ago by ▴ 20
0
votes
3
replies
720
views
How can I use KING on windows ?
plink king
updated 4 days ago by 39k • written 4.1 years ago by ▴ 20
0
votes
5
replies
707
views
vcftools --weir-fst-pop returns -nan
fst vcftools
updated 6 days ago by • 0 • written 5 months ago by • 0
1
vote
3
replies
702
views
Regular Expression for conversion
Linux grep
updated 5 days ago by 21k • written 19 months ago by ▴ 10
2
votes
3
replies
690
views
Including bioinformatics into an agriculture/horticulture dissertation project
agrobioinformatics plant-gene-analysis
updated 5 days ago by 39k • written 4.1 years ago by • 0
0
votes
1
reply
679
views
Small demo bioinformatics workflows which don't require reference data?
workflow pipeline
updated 2 days ago by 39k • written 3.7 years ago by ★ 3.3k
0
votes
0
replies
643
views
What option should I use for show me result which I can filter my data by their p-value and FC?
MASIGPRO Time-Course RNA-Seq
updated 5 days ago by 39k • written 3.4 years ago by ▴ 70
0
votes
0
replies
642
views
time Course RNa-seq data from peripheral blood
time-course RNA-Seq
updated 5 days ago by 39k • written 4.0 years ago by ▴ 70
0
votes
0
replies
613
views
Tools for mRNA-Seq time series DGE GCN and other analyses
time-course RNA-Seq time-series
updated 5 days ago by 39k • written 3.1 years ago by ▴ 560
0
votes
2
replies
608
views
ERROR running Cuffmerge in reference based RNA-SEQ analysis?
cuffmerge RNA-Seq Cufflinks
updated 5 days ago by 39k • written 13 months ago by • 0
0
votes
0
replies
587
views
Proportion of traits in several groups
propotion-test fishers-exact-test
updated 2 days ago by 39k • written 3.8 years ago by ▴ 140
0
votes
7
replies
564
views
How to deal with duplicated gene IDs in TCGA RNA expression data?
TCGA Expression mRNA
updated 5 days ago by ★ 2.9k • written 9 days ago by ▴ 30
0
votes
0
replies
535
views
Online courses/studies bioinformatics
online-study learning
updated 2 days ago by 39k • written 3.8 years ago by • 0
0
votes
2
replies
520
views
1-way-2-fold cross family analysis
cross-family-analysis
updated 4 days ago by 39k • written 3.8 years ago by ▴ 20
144 results • Page 1 of 3
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Answer: How to calculate TPM from featureCounts output
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A: How To Predict Pseudogenes In A Genome
How To Predict Pseudogenes In A Genome
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Recent Replies
Answer: Getting species names and taxa id from assembly accession number by MirianT_NCBI ▴ 580
Hi, As an alternative, you could use [NCBI Datasets][1] for this task. NCBI Datasets allows users to retrieve metadata reports in JSON or…
Comment: Optimum setting for local blastp for ~10K sequences by sodiumnitrate ▴ 20
Thank you for the info! It turned out that running all 10k at once is actually faster than running one or two at a time!
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!
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