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Biostar手册:第2版-The Biostar Handbook: 2nd Edition文件编号:75

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标题(title):The Biostar Handbook: 2nd Edition
Biostar手册:第2版
作者(author):Dr. István Albert
出版社(publisher):
大小(size):37 MB (39262219 bytes)
格式(extension):pdf
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Table of contents :
I Preface......Page 32
Online courses......Page 34
Access your account......Page 35
Who is a Biostar?......Page 36
About the author......Page 38
What is this book about?......Page 41
What is covered in the book?......Page 42
What subfields of bioinformatics exist?......Page 43
Is there a list of functional assays used in bioinformatics?......Page 45
But what is bioinformatics, really?......Page 46
Is creativity required to succeed?......Page 47
What type of computer is required?......Page 48
Can I learn bioinformatics from this book?......Page 49
How long will it take me to learn bioinformatics?......Page 50
Biology for bioinformaticians......Page 51
What is DNA?......Page 52
What is sense/antisense?......Page 54
What is a genome's purpose?......Page 55
How does a genome function?......Page 56
What is a protein?......Page 57
What is an ORF?......Page 58
Do genomes have other features?......Page 59
What is homology?......Page 60
What is the recommended computer for bioinformatics?......Page 62
What about the cloud?......Page 63
Are there alternatives to using Unix?......Page 64
What is Bioconductor?......Page 65
What is Galaxy?......Page 66
Are commercial bioinformatics software packages expensive?......Page 67
Should I freelance as a bioinformatician?......Page 68
What do bioinformaticians look like?......Page 69
How do I perform a holistic analysis?......Page 70
What are the rules of a bioinformatics analysis?......Page 71
What does simple mean?......Page 72
How to deal with anxiety and stress?......Page 73
II Installation......Page 75
Is this going to be difficult?......Page 77
What are environments?......Page 78
What is bioconda?......Page 79
How do I check that Entrez Direct works?......Page 80
How do I verify that all other programs work?......Page 81
How do I report installation problems?......Page 82
How do I install a new tool?......Page 83
How should I set up my file structure?......Page 84
What to do if I get stuck?......Page 85
What features should my text editor have?......Page 86
Super annoying behaviors......Page 87
Which text editor to choose?......Page 88
Watch the line endings on Windows!......Page 89
III UNIX COMMAND LINE......Page 90
What does the command line look like?......Page 92
Is the command line hard to learn?......Page 93
What is a shell?......Page 94
What is the best way to learn Unix?......Page 96
Where can I learn more about the shell?......Page 97
Why Unix?......Page 98
1. The Terminal......Page 99
3: The Unix tree......Page 101
5: Making new directories......Page 102
7: The root directory......Page 103
8: Navigating upwards in the Unix filesystem......Page 104
10: Finding your way back home......Page 105
11: Making the ls command more useful......Page 106
13: Removing directories......Page 107
15: Creating empty files with the touch command......Page 108
17: Renaming files......Page 109
19: Removing files......Page 110
21: Copying directories......Page 111
23: Viewing files with cat......Page 112
25: Editing small text files with nano......Page 113
26: The $PATH environment variable......Page 114
27: Matching lines in files with grep......Page 115
Miscellaneous Unix power commands......Page 116
What directory should I use?......Page 118
Where are we getting the data from?......Page 119
How do I obtain a data file that is online?......Page 120
How many feature types are in this data?......Page 125
One-liners......Page 126
What objects may be compressed?......Page 128
How do I compress or uncompress a file?......Page 129
How do I compress or uncompress multiple files?......Page 130
What is a tarbomb?......Page 131
How do we use tar again?......Page 132
IV DATA SOURCES......Page 133
Essential properties of data......Page 135
What is the state of data in bioinformatics?......Page 136
What kind of problems does bioinformatics data have?......Page 137
How complete is the data that will I obtain?......Page 139
Final thoughts on data......Page 140
What are the major DNA data repositories?......Page 142
What kind of other data sources are there?......Page 144
What's in a name?......Page 145
Project systematic names......Page 146
A Quick look at the GENBANK format.......Page 147
A quick look at the FASTQ format......Page 148
A quick look at the GFF/GTF/BED formats......Page 149
Can I convert between formats.......Page 150
What are genomic builds?......Page 151
Should download data first or get data on-demand?......Page 152
How many genomic builds does the human genome have?......Page 153
How do we transfer genomic coordinates between builds?......Page 154
Human gene naming......Page 155
Is there a better resource for human annotations?......Page 156
What can I get from ENSEMBL?......Page 157
What a working strategy for finding reference information......Page 158
What is Entrez?......Page 159
How is data organized in NCBI?......Page 160
How do I use Entrez Direct?......Page 161
How do we search with Entrez Direct?......Page 162
How to do more work with Entrez Direct?......Page 163
How do I use efetch?......Page 164
How do I get run information on a project?......Page 165
How do I extract taxonomy information?......Page 166
V DATA FORMATS......Page 168
Should I re-format (transform) my data?......Page 170
When to re-format (transform) data?......Page 172
What is the GenBank format?......Page 173
How are RefSeq sequences named?......Page 174
What is the FASTA format?......Page 178
Are there problems with this format?......Page 179
Is there more information in the FASTA sequences?......Page 180
Where do I get a fasta file?......Page 181
What is the FASTQ format?......Page 182
How to recognize FASTQ qualities by eye......Page 183
Is there more information in FASTQ headers?......Page 184
How do I convert FASTQ quality codes at the command line?......Page 185
Closing thoughts on FASTQ......Page 186
Advanced FASTQ processing......Page 187
How do I get the GC content?......Page 188
How do I find FASTA/Q sequences containing degenerate bases and locate them?......Page 189
How do I locate motif/subsequence/enzyme digest sites in FASTA/Q sequence?......Page 190
How do I split FASTA sequences according to information in the header?......Page 191
How do I search and replace within a FASTA header using character strings from a text file?......Page 192
How do I extract paired reads from two paired-end reads files?......Page 193
How to concatenate two FASTA sequences in to one?......Page 194
VI VISUALIZING DATA......Page 196
What are the challenges of visualization?......Page 198
Why are default browser screens so complicated?......Page 199
How do I interpret glyphs?......Page 200
What about online genome browsers?......Page 201
What is IGV?......Page 202
What data does IGV come with?......Page 203
How do I create a custom genome in IGV?......Page 204
VII SEQUENCE ONTOLOGY......Page 206
Why is the ontology necessary?......Page 208
Who names the genes?......Page 209
What will our data tell us?......Page 210
Where do I see Sequence Ontology (SO) terms used?......Page 211
How do I access the Sequence Ontology browser?......Page 212
How are the SO relationships defined?......Page 214
How can I quickly search the Sequence Ontology?......Page 215
How to search for other information?......Page 216
VIII GENE ONTOLOGY......Page 218
How is the GO designed?......Page 220
What kind of properties do annotated gene products have ?......Page 221
How are GO terms organized?......Page 222
Where can the visualize GO terms online?......Page 224
What does a GO term file contain?......Page 227
Where can I find the association files for different organisms?......Page 228
What format does the GO association file have?......Page 229
What kind of properties does the GO data have?......Page 230
What are the most annotated human genes and proteins?......Page 231
What are the ten most highly annotated genes in the GO dataset?......Page 232
How complete is the GO?......Page 233
The sorry state of data categorization......Page 235
What is an Over-Representation Analysis (ORA)?......Page 236
Are there different ways to compute ORA analyses?......Page 237
What is a Functional Class Scoring (FCS)?......Page 239
Should I trust the results of functional analyses?......Page 240
What tools are used to perform enrichment analysis?......Page 241
Will different tools produce different results?......Page 242
How do I perform a gene set enrichment analysis?......Page 243
How to use AgriGO......Page 245
How to use SEA?......Page 246
How do I prepare a custom annotation for AgriGO?......Page 247
What is a standout feature of the g:Profiler?......Page 251
What functionality does the g:Profile have?......Page 252
How to use g:profiler at the command line......Page 254
Authors note......Page 256
What are the different steps in a DAVID analysis?......Page 257
How do I start an analysis with DAVID?......Page 258
What is the Functional Annotation Summary?......Page 259
What is a Functional Annotation Chart ?......Page 260
What is Functional Annotation Clustering?......Page 261
What is the Gene Functional Classification Tool?......Page 262
What is an EASE Score?......Page 264
What are some pros and cons of DAVID?......Page 265
Plot GO terms......Page 267
Finding enrichment with goatools......Page 272
How to use ErmineJ......Page 276
What are the annotation files?......Page 277
What is a gene score file?......Page 278
How do I start an analysis in ErmineJ?......Page 279
What is an Over-Representation Analysis (ORA)?......Page 280
What are the results of an ORA analysis?......Page 281
Is multi-functionality good or bad?......Page 283
What is Gene Score Resampling (GSR)?......Page 284
What is Correlation Analysis in ErmineJ?......Page 285
IX REPRODUCIBILITY......Page 286
What is the red herring of reproducibility?......Page 288
Is science
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